Running as unit: rb-build-arm64_20-38690.service ==================================================================================== Fri Sep 27 01:36:47 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_20) on jenkins, called using "codethink02-arm64 codethink04-arm64" as arguments. Fri Sep 27 01:36:47 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-cFvSFGEb" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 01:36:47 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Fri Sep 27 01:36:47 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-bbQrdo' Fri Sep 27 01:36:47 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Sep 27 01:36:47 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-RviRKU' ok, let's check if pyranges is building anywhere yet… ok, pyranges is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of pyranges in trixie on arm64 on jenkins now. 1st build will be done on codethink02-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Fri Sep 27 01:37:04 UTC 2024 I: starting to build pyranges/trixie/arm64 on jenkins on '2024-09-27 01:36' Fri Sep 27 01:37:04 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/38690/console.log 1727401024 arm64 trixie pyranges Fri Sep 27 01:37:04 UTC 2024 I: Downloading source for trixie/pyranges=0.0.111+ds-8 --2024-09-27 01:37:04-- http://deb.debian.org/debian/pool/main/p/pyranges/pyranges_0.0.111%2bds-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2428 (2.4K) [text/prs.lines.tag] Saving to: ‘pyranges_0.0.111+ds-8.dsc’ 0K .. 100% 291M=0s 2024-09-27 01:37:04 (291 MB/s) - ‘pyranges_0.0.111+ds-8.dsc’ saved [2428/2428] --2024-09-27 01:37:04-- http://deb.debian.org/debian/pool/main/p/pyranges/pyranges_0.0.111%2bds-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2428 (2.4K) [text/prs.lines.tag] Saving to: ‘pyranges_0.0.111+ds-8.dsc’ 0K .. 100% 291M=0s 2024-09-27 01:37:04 (291 MB/s) - ‘pyranges_0.0.111+ds-8.dsc’ saved [2428/2428] Fri Sep 27 01:37:04 UTC 2024 I: pyranges_0.0.111+ds-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pyranges Binary: python3-pyranges Architecture: all Version: 0.0.111+ds-8 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Étienne Mollier Homepage: https://github.com/biocore-ntnu/pyranges Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/pyranges Vcs-Git: https://salsa.debian.org/med-team/pyranges.git Testsuite: autopkgtest-pkg-python Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-ncls , python3-pyrle , python3-pytest , python3-pytest-xdist , python3-sorted-nearest, python3-hypothesis, bedtools, samtools Package-List: python3-pyranges deb python optional arch=all Checksums-Sha1: 3591cd303505955df6c34eec755d51f27bd38e5b 3288424 pyranges_0.0.111+ds.orig.tar.xz 11c16ff4e96765e90b03b8970baf6a2a67a79508 83524 pyranges_0.0.111+ds-8.debian.tar.xz Checksums-Sha256: b22a50cb9e0109c8c14720385a5e87bef029f491d4f3e02dbe492866802144d1 3288424 pyranges_0.0.111+ds.orig.tar.xz 32f2fd274b0a1491c14271918ced0d65f4f54803de208b204d1b7e3d72c1e2da 83524 pyranges_0.0.111+ds-8.debian.tar.xz Files: 2c48870491f89e171b4aeeaa5b3b216a 3288424 pyranges_0.0.111+ds.orig.tar.xz af00bef0cfbf5e3b80414fb319855373 83524 pyranges_0.0.111+ds-8.debian.tar.xz Dgit: 695bcedb7bdf86c3affa56de602d2bfb26c335dd debian archive/debian/0.0.111+ds-8 https://git.dgit.debian.org/pyranges -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbus6QUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdq8Ow//Wvl+goyl2sk6S9YQ4rupm9O9dr5x gH4amgn/SZvJJyeS/FDigQO8Gk7H4eOAVqUDixAW345RzTg8A24FUp1RfYl0jGK7 yYxvyOqbwspMqMPRfshEYTdE4e8EeRgcT8hBgxx1S4XJKHKmIccalG/car77mqA9 1wGYoJu+3/33hDJr03Pj4YvINMldqYrEpImE5xXajpNY7tyAEqkJ5s2BQzN5X9MH oipETIoa2BqMMcSSIVzHaxM4KskGuDAT0t7VG/J2lZtTAkszZUrCeKKfaEgKCWrm UxfxkGQTuua9v1VjsHsam1U2VOXYYDdpFo99GMyv9jw4Xzir6KxGHJhfyYjM4q/L 2Kg6Z4iQh2uL/w34ai+cuxkFvt8yRLMhWfWUcL9VC8HrLRurEH55eKUafQ/WrGth kKdKfLNKSoYsXos/b1jjv9jR7M57eKblXzHjYgTaZH5NQWxONJRmj5NQf47UvEYr TDhP193+vbWKz5WteTXgY3MhIf5qQNNfNJIP+LhG1jCb3N/Ktk0PlkRFcbFuLLdq +uusJ+9iW4w3FdsMxK52AIw78aAChS57N9xX1bBTp79oL4NfF7jUPF6swV4qax+j HlfsPHexQAGSEHGb8kym9PgywQ1Ak30ZrBjqjxjU8JDCgH7LFVBZs1OXQMj2lcsi h67qJRAM6vTfQJg= =i+Dk -----END PGP SIGNATURE----- Fri Sep 27 01:37:04 UTC 2024 I: Checking whether the package is not for us Fri Sep 27 01:37:04 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Fri Sep 27 01:37:04 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Fri Sep 27 01:37:04 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Fri Sep 27 01:37:04 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-l7Eyuo' ==================================================================================== Fri Sep 27 01:37:06 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "1 pyranges trixie /srv/reproducible-results/rbuild-debian/r-b-build.mqzlEEs2 0.0.111+ds-8" as arguments. Fri Sep 27 01:37:06 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-7OrYZfFO" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 27 01:37:06 UTC 2024 I: Downloading source for trixie/pyranges=0.0.111+ds-8 Reading package lists... NOTICE: 'pyranges' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pyranges.git Please use: git clone https://salsa.debian.org/med-team/pyranges.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3374 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main pyranges 0.0.111+ds-8 (dsc) [2428 B] Get:2 http://deb.debian.org/debian trixie/main pyranges 0.0.111+ds-8 (tar) [3288 kB] Get:3 http://deb.debian.org/debian trixie/main pyranges 0.0.111+ds-8 (diff) [83.5 kB] Fetched 3374 kB in 0s (84.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'pyranges' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pyranges.git Please use: git clone https://salsa.debian.org/med-team/pyranges.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3374 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main pyranges 0.0.111+ds-8 (dsc) [2428 B] Get:2 http://deb.debian.org/debian trixie/main pyranges 0.0.111+ds-8 (tar) [3288 kB] Get:3 http://deb.debian.org/debian trixie/main pyranges 0.0.111+ds-8 (diff) [83.5 kB] Fetched 3374 kB in 0s (84.2 MB/s) Download complete and in download only mode ============================================================================= Building pyranges in trixie on arm64 on codethink02-arm64 now. Date: Fri Sep 27 02:37:06 BST 2024 Date UTC: Fri Sep 27 01:37:06 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 26 13:37:07 -12 2024 I: pbuilder-time-stamp: 1727401027 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pyranges_0.0.111+ds-8.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Sep 21 11:53:08 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyranges_0.0.111+ds-8.dsc: no acceptable signature found dpkg-source: info: extracting pyranges in pyranges-0.0.111+ds dpkg-source: info: unpacking pyranges_0.0.111+ds.orig.tar.xz dpkg-source: info: unpacking pyranges_0.0.111+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_dtype.patch dpkg-source: info: applying reorder.patch dpkg-source: info: applying numpy_1.24.patch dpkg-source: info: applying healthcheck-all.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying pandas2.0.patch dpkg-source: info: applying fix-test_unary.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1596758/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='95b946540b07430d823bdeb3be0c2c6c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1596758' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.mqzlEEs2/pbuilderrc_lHEG --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mqzlEEs2/b1 --logfile b1/build.log pyranges_0.0.111+ds-8.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1596758/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-ncls, python3-pyrle, python3-pytest, python3-pytest-xdist, python3-sorted-nearest, python3-hypothesis, bedtools, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-ncls; however: Package python3-ncls is not installed. pbuilder-satisfydepends-dummy depends on python3-pyrle; however: Package python3-pyrle is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-sorted-nearest; however: Package python3-sorted-nearest is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-autocommand{a} python3-dateutil{a} python3-execnet{a} python3-hypothesis{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-natsort{a} python3-ncls{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyrle{a} python3-pytest{a} python3-pytest-xdist{a} python3-setuptools{a} python3-six{a} python3-sorted-nearest{a} python3-sortedcontainers{a} python3-tabulate{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-click python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget 0 packages upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After unpacking 211 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.5-1+b1 [26.9 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.5-1+b1 [9872 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.5-1+b1 [27.9 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 bedtools arm64 2.31.1+dfsg-2 [588 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240824 [109 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.10.1-1 [329 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-3 [362 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2 [95.7 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.5-1+b1 [1048 B] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-attr all 23.2.0-2 [65.5 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-7 [16.4 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-execnet all 2.1.1-1 [40.2 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-hypothesis all 6.112.0-1 [320 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-natsort all 8.0.2-2 [39.0 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-ncls arm64 0.0.63-hotfix+ds-1+b5 [339 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.2.2+dfsg-4+b1 [3571 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.2.2+dfsg-4 [3095 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 python3-pyrle arm64 0.0.33-4.1+b1 [263 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 python3-sorted-nearest arm64 0.0.39+dfsg-2+b1 [274 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3 [624 kB] Fetched 44.8 MB in 0s (124 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1+b1_arm64.deb ... Unpacking python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.5-1+b1) ... Setting up python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21289 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.5-1+b1_arm64.deb ... Unpacking python3 (3.12.5-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package bedtools. Preparing to unpack .../16-bedtools_2.31.1+dfsg-2_arm64.deb ... Unpacking bedtools (2.31.1+dfsg-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../23-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../25-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../31-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../32-python3-more-itertools_10.4.0-1_all.deb ... Unpacking python3-more-itertools (10.4.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../33-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../34-python3-typeguard_4.3.0-1_all.deb ... Unpacking python3-typeguard (4.3.0-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../35-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../36-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../37-python3-jaraco.functools_4.0.2-1_all.deb ... Unpacking python3-jaraco.functools (4.0.2-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../38-python3-pkg-resources_74.1.2-2_all.deb ... Unpacking python3-pkg-resources (74.1.2-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../39-python3-zipp_3.20.2-1_all.deb ... Unpacking python3-zipp (3.20.2-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../40-python3-setuptools_74.1.2-2_all.deb ... Unpacking python3-setuptools (74.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../41-dh-python_6.20240824_all.deb ... Unpacking dh-python (6.20240824) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../42-libblas3_3.12.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3) ... Selecting previously unselected package libbrotli1:arm64. 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Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../49-libngtcp2-16_1.6.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../50-libngtcp2-crypto-gnutls8_1.6.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../51-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../52-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../53-libssh2-1t64_1.11.0-7_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-7) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../54-libcurl3t64-gnutls_8.10.1-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.10.1-1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../55-libdeflate0_1.21-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.21-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../56-libgfortran5_14.2.0-3_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-3) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../57-libhtscodecs2_1.6.1-1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.1-1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../58-libhts3t64_1.20+ds-1_arm64.deb ... Unpacking libhts3t64:arm64 (1.20+ds-1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../59-liblapack3_3.12.0-3_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../60-libncurses6_6.5-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5-2) ... Selecting previously unselected package python3-all. Preparing to unpack .../61-python3-all_3.12.5-1+b1_arm64.deb ... Unpacking python3-all (3.12.5-1+b1) ... Selecting previously unselected package python3-attr. Preparing to unpack .../62-python3-attr_23.2.0-2_all.deb ... Unpacking python3-attr (23.2.0-2) ... Selecting previously unselected package python3-six. Preparing to unpack .../63-python3-six_1.16.0-7_all.deb ... Unpacking python3-six (1.16.0-7) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../64-python3-dateutil_2.9.0-2_all.deb ... Unpacking python3-dateutil (2.9.0-2) ... Selecting previously unselected package python3-execnet. Preparing to unpack .../65-python3-execnet_2.1.1-1_all.deb ... Unpacking python3-execnet (2.1.1-1) ... Selecting previously unselected package python3-sortedcontainers. 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Selecting previously unselected package python3-packaging. Preparing to unpack .../72-python3-packaging_24.1-1_all.deb ... Unpacking python3-packaging (24.1-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../73-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-pandas-lib:arm64. Preparing to unpack .../74-python3-pandas-lib_2.2.2+dfsg-4+b1_arm64.deb ... Unpacking python3-pandas-lib:arm64 (2.2.2+dfsg-4+b1) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../75-python3-pandas_2.2.2+dfsg-4_all.deb ... Unpacking python3-pandas (2.2.2+dfsg-4) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../76-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-tabulate. Preparing to unpack .../77-python3-tabulate_0.9.0-1_all.deb ... Unpacking python3-tabulate (0.9.0-1) ... Selecting previously unselected package python3-pyrle. Preparing to unpack .../78-python3-pyrle_0.0.33-4.1+b1_arm64.deb ... Unpacking python3-pyrle (0.0.33-4.1+b1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../79-python3-pytest_8.3.3-1_all.deb ... Unpacking python3-pytest (8.3.3-1) ... Selecting previously unselected package python3-pytest-xdist. Preparing to unpack .../80-python3-pytest-xdist_3.6.1-1_all.deb ... Unpacking python3-pytest-xdist (3.6.1-1) ... Selecting previously unselected package python3-sorted-nearest. Preparing to unpack .../81-python3-sorted-nearest_0.0.39+dfsg-2+b1_arm64.deb ... Unpacking python3-sorted-nearest (0.0.39+dfsg-2+b1) ... Selecting previously unselected package samtools. Preparing to unpack .../82-samtools_1.20-3_arm64.deb ... Unpacking samtools (1.20-3) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b4) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.63.0-1) ... Setting up libdeflate0:arm64 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Sep 27 01:37:42 UTC 2024. Universal Time is now: Fri Sep 27 01:37:42 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:arm64 (6.5-2) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-3) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.4.0-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libssh2-1t64:arm64 (1.11.0-7) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.10.1-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libhts3t64:arm64 (1.20+ds-1) ... Setting up libpython3.12-stdlib:arm64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:arm64 (3.12.5-1+b1) ... Setting up python3 (3.12.5-1+b1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-natsort (8.0.2-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-packaging (24.1-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-execnet (2.1.1-1) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-hypothesis (6.112.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.12.5-1+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-pytest-xdist (3.6.1-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b5) ... Setting up dh-python (6.20240824) ... Setting up python3-pandas-lib:arm64 (2.2.2+dfsg-4+b1) ... Setting up python3-sorted-nearest (0.0.39+dfsg-2+b1) ... Setting up python3-pandas (2.2.2+dfsg-4) ... Setting up python3-pyrle (0.0.33-4.1+b1) ... Processing triggers for libc-bin (2.40-2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-8_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyranges-0.0.111+ds' echo 'Generating corresponding files ...' Generating corresponding files ... cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai make[1]: Leaving directory '/build/reproducible-path/pyranges-0.0.111+ds' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/*.bed /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/test_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges '/build/reproducible-path/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/chip_10.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/gencode.gff3' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/exons.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/bw.bw' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/cpg.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/lamina.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam.bai' I: pybuild base:311: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 12 ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/.hypothesis/examples')) rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: xdist-3.6.1, hypothesis-6.112.0, typeguard-4.3.0 created: 12/12 workers 12 workers [531 items] scheduling tests via LoadScheduling tests/test_binary.py::test_coverage[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_nearest[None-False-opposite] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/data/test_data.py::test_all_data [gw0] [ 0%] PASSED tests/data/test_data.py::test_all_data tests/test_binary.py::test_set_intersect[False] [gw7] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] [gw6] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] [gw11] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] [gw9] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] [gw5] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] [gw10] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] [gw7] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] [gw6] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] [gw10] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] [gw5] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] [gw9] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] [gw7] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] [gw6] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] [gw11] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] [gw7] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] [gw10] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] [gw5] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] [gw9] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] [gw6] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] [gw11] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] [gw10] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] [gw5] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] [gw7] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] [gw9] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] [gw6] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] [gw5] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] [gw10] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] [gw11] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] [gw6] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw7] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] [gw5] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] [gw10] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] [gw9] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] [gw11] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] [gw6] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw5] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] [gw7] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] [gw10] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] [gw9] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] [gw6] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] [gw5] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] [gw11] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] [gw10] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] [gw7] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] [gw9] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] [gw6] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] [gw5] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] [gw10] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] [gw6] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] [gw7] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] [gw11] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] [gw10] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] [gw9] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] [gw5] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] [gw6] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] [gw1] [ 10%] PASSED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_nearest[downstream-False-opposite] [gw10] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] [gw3] [ 11%] PASSED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_nearest[upstream-True-False] [gw5] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] [gw11] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw6] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] [gw9] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] [gw7] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] [gw10] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] [gw5] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] [gw11] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw6] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] [gw9] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] [gw10] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] [gw0] [ 13%] PASSED tests/test_binary.py::test_set_intersect[False] tests/test_binary.py::test_set_intersect[same] [gw7] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] [gw11] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] [gw6] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] [gw9] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] [gw7] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] [gw5] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw11] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] [gw2] [ 14%] PASSED tests/test_binary.py::test_coverage[False] [gw6] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_binary.py::test_coverage[same] [gw4] [ 15%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw10] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] [gw9] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] [gw7] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] [gw5] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw6] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] [gw11] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] [gw9] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] [gw7] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] [gw6] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] [gw10] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] [gw5] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] [gw9] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] [gw7] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] [gw11] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] [gw6] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] [gw7] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] [gw9] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] [gw10] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] [gw5] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] [gw11] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] [gw6] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] [gw7] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] [gw9] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] [gw5] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] [gw10] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] [gw7] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] [gw11] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] [gw6] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] [gw9] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] [gw7] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] [gw6] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] [gw11] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] [gw1] [ 21%] PASSED tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_binary.py::test_jaccard[False] [gw9] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] [gw5] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] [gw10] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] [gw11] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] [gw6] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] [gw7] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] [gw9] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw5] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw6] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] [gw11] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] [gw9] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] [gw10] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] [gw7] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] [gw5] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] [gw6] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] [gw11] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] [gw3] [ 24%] PASSED tests/test_binary.py::test_nearest[upstream-True-False] tests/test_binary.py::test_nearest[upstream-True-same] [gw7] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] [gw10] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] [gw6] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] [gw5] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] [gw11] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] [gw9] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] [gw6] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] [gw7] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] [gw0] [ 26%] PASSED tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_set_union[False] [gw11] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] [gw10] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] [gw5] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] [gw7] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] [gw9] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] [gw6] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] [gw10] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] [gw5] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] [gw10] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] [gw7] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] [gw8] [ 28%] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] [gw11] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw5] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] [gw9] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw6] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] [gw10] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] [gw7] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] [gw5] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] [gw10] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] [gw9] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] [gw7] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] [gw11] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] [gw6] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] [gw2] [ 30%] PASSED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_coverage[opposite] [gw9] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] [gw10] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] [gw7] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] [gw5] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] [gw11] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] [gw9] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw7] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] [gw10] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] [gw5] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] [gw6] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw9] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] [gw11] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] [gw4] [ 33%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw7] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw1] [ 33%] PASSED tests/test_binary.py::test_jaccard[False] tests/test_binary.py::test_jaccard[same] [gw10] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] [gw5] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] [gw7] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] [gw11] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw6] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] [gw9] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] [gw10] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] [gw7] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] [gw11] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] [gw5] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] [gw10] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] [gw6] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] [gw7] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] [gw11] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] [gw9] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] [gw3] [ 36%] PASSED tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw10] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] [gw6] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] [gw11] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] [gw7] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] [gw5] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] [gw9] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] [gw11] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] [gw6] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] [gw7] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] [gw10] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] [gw5] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] [gw11] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] [gw6] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] [gw7] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] [gw10] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] [gw5] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] [gw9] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] [gw7] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] [gw6] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] [gw11] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] [gw10] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] [gw5] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] [gw7] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] [gw9] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] [gw11] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] [gw6] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] [gw10] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] [gw5] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] [gw0] [ 42%] PASSED tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_set_union[same] [gw7] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] [gw5] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] [gw10] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] [gw6] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] [gw11] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw7] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] [gw9] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] [gw10] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] [gw11] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw6] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] [gw5] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] [gw7] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] [gw6] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] [gw10] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] [gw1] [ 45%] PASSED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw9] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] [gw2] [ 45%] PASSED tests/test_binary.py::test_coverage[opposite] tests/test_binary.py::test_subtraction[same] [gw7] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] [gw5] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] [gw10] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] [gw6] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] [gw11] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] [gw7] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] [gw9] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] [gw6] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] [gw10] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] [gw7] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] [gw3] [ 47%] PASSED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw5] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] [gw9] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] [gw6] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] [gw10] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] [gw11] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] [gw7] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] [gw9] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] [gw6] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] [gw10] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] [gw7] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] [gw5] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] [gw11] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] [gw6] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] [gw10] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] [gw7] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] [gw9] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] [gw11] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] [gw10] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] [gw7] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] [gw5] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] [gw9] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] [gw6] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] [gw7] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] [gw8] [ 51%] PASSED tests/test_binary.py::test_k_nearest[None-True-opposite-last] tests/test_binary.py::test_k_nearest[None-True-same-last] [gw10] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] [gw11] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] [gw4] [ 52%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw6] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] [gw9] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] [gw5] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] [gw7] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] [gw10] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] [gw6] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw9] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] [gw7] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] [gw11] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] [gw10] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] [gw6] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw5] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] [gw9] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] [gw7] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] [gw10] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] [gw6] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw0] [ 55%] PASSED tests/test_binary.py::test_set_union[same] tests/test_binary.py::test_overlap[False] [gw5] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] [gw11] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] [gw1] [ 56%] PASSED tests/test_binary.py::test_join[False] tests/test_binary.py::test_join[same] [gw7] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] [gw10] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] [gw9] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] [gw6] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] [gw11] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] [gw7] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] [gw5] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] [gw6] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] [gw7] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] [gw9] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] [gw11] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] [gw10] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] [gw6] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] [gw5] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] [gw7] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw9] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] [gw6] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] [gw10] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] [gw3] [ 59%] PASSED tests/test_binary.py::test_nearest[upstream-False-False] tests/test_binary.py::test_nearest[upstream-False-same] [gw7] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw11] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] [gw5] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] [gw6] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] [gw10] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw7] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] [gw9] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] [gw5] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] [gw11] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] [gw6] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] [gw2] [ 61%] PASSED tests/test_binary.py::test_subtraction[same] tests/test_binary.py::test_subtraction[opposite] [gw10] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] [gw7] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] [gw5] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] [gw6] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] [gw9] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] [gw11] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] [gw10] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] [gw7] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] [gw5] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] [gw9] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] [gw6] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] [gw10] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] [gw11] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] [gw7] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] [gw0] [ 64%] PASSED tests/test_binary.py::test_overlap[False] tests/test_binary.py::test_overlap[same] [gw5] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] [gw6] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] [gw9] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] [gw4] [ 65%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] tests/test_binary.py::test_k_nearest[upstream-False-same-last] [gw5] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] [gw10] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw7] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] [gw9] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] [gw11] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] [gw6] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] [gw1] [ 66%] PASSED tests/test_binary.py::test_join[same] tests/test_binary.py::test_join[opposite] [gw10] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw7] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] [gw5] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] [gw9] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] [gw11] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] [gw10] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] [gw7] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] [gw6] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] [gw9] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] [gw10] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] [gw5] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] [gw7] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] [gw6] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] [gw11] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] [gw5] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] [gw10] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] [gw9] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] [gw7] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] [gw6] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] [gw3] [ 70%] PASSED tests/test_binary.py::test_nearest[upstream-False-same] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw11] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] [gw10] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] [gw9] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] [gw5] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] [gw7] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] [gw6] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] [gw11] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] [gw10] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] [gw5] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] [gw7] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] [gw11] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] [gw9] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] [gw6] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] [gw10] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] [gw0] [ 73%] PASSED tests/test_binary.py::test_overlap[same] tests/test_binary.py::test_overlap[opposite] [gw7] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] [gw9] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] [gw6] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] [gw5] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] [gw11] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] [gw10] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] [gw9] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw7] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] [gw6] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] [gw1] [ 75%] PASSED tests/test_binary.py::test_join[opposite] tests/test_binary.py::test_reldist [gw11] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] [gw5] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] [gw10] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] [gw9] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] [gw7] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] [gw11] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] [gw5] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] [gw6] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] [gw11] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] [gw10] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] [gw9] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] [gw7] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] [gw5] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] [gw8] [ 77%] PASSED tests/test_binary.py::test_k_nearest[None-True-same-last] [gw2] [ 78%] PASSED tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_k_nearest[None-True-False-last] [gw11] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] [gw6] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] [gw5] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] [gw4] [ 78%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw7] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] [gw10] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] [gw9] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] [gw6] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] [gw11] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] [gw5] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] [gw10] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] [gw6] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] [gw7] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] [gw9] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] [gw3] [ 80%] PASSED tests/test_binary.py::test_nearest[upstream-False-opposite] tests/test_binary.py::test_nearest[downstream-True-False] [gw5] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] [gw6] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] [gw0] [ 81%] PASSED tests/test_binary.py::test_overlap[opposite] tests/test_binary.py::test_intersect[False] [gw11] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] [gw9] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] [gw10] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] [gw7] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] [gw5] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] [gw6] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] [gw11] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] [gw9] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] [gw7] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] [gw1] [ 83%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw10] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] [gw5] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] [gw6] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] [gw9] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] [gw11] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] [gw10] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] [gw7] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] [gw5] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] [gw6] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] [gw9] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] [gw11] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] [gw10] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] [gw7] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] [gw6] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] [gw5] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] [gw11] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] [gw9] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] [gw7] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] [gw10] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] [gw6] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw9] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] [gw11] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] [gw5] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] [gw10] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] [gw7] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] [gw9] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] [gw11] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] tests/test_genomicfeatures.py::test_introns_single [gw5] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] tests/test_getset_attr.py::test_getsetattr [gw5] [ 88%] PASSED tests/test_getset_attr.py::test_getsetattr tests/test_io.py::test_read_bed [gw5] [ 89%] PASSED tests/test_io.py::test_read_bed tests/test_pickle.py::test_pickle [gw5] [ 89%] PASSED tests/test_pickle.py::test_pickle tests/test_stranded.py::test_stranded [gw6] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw5] [ 89%] PASSED tests/test_stranded.py::test_stranded tests/test_stranded.py::test_unstrand tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] [gw5] [ 89%] PASSED tests/test_stranded.py::test_unstrand tests/test_unary.py::test_merge[True] [gw10] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] tests/test_getset_attr.py::test_getsetattr_fails [gw10] [ 90%] PASSED tests/test_getset_attr.py::test_getsetattr_fails tests/test_unary.py::test_cluster[False] [gw7] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] tests/test_getset_attr.py::test_getsetattr_with_str [gw7] [ 90%] PASSED tests/test_getset_attr.py::test_getsetattr_with_str tests/test_unary.py::test_cluster_by[False] [gw9] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] tests/test_io.py::test_read_gtf [gw9] [ 90%] PASSED tests/test_io.py::test_read_gtf tests/test_unary.py::test_merge_by[False] [gw11] [ 91%] PASSED tests/test_genomicfeatures.py::test_introns_single tests/test_io.py::test_read_gff3 [gw11] [ 91%] PASSED tests/test_io.py::test_read_gff3 tests/test_unary.py::test_init[True] [gw6] [ 91%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] tests/test_unary.py::test_merge[False] [gw0] [ 91%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_intersect[same] [gw2] [ 91%] PASSED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw11] [ 92%] PASSED tests/test_unary.py::test_init[True] tests/test_unary.py::test_init[False] [gw4] [ 92%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-False-last] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw3] [ 92%] PASSED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_binary.py::test_nearest[downstream-True-same] [gw11] [ 92%] PASSED tests/test_unary.py::test_init[False] tests/test_unary.py::test_summary [gw1] [ 92%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw5] [ 93%] PASSED tests/test_unary.py::test_merge[True] tests/test_unary.py::test_cluster[True] [gw6] [ 93%] PASSED tests/test_unary.py::test_merge[False] tests/test_unary.py::test_getitem [gw0] [ 93%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw9] [ 93%] PASSED tests/test_unary.py::test_merge_by[False] tests/test_unary.py::test_windows [gw11] [ 93%] PASSED tests/test_unary.py::test_summary tests/windows/test_windows.py::test_windows [gw11] [ 93%] PASSED tests/windows/test_windows.py::test_windows [gw6] [ 94%] PASSED tests/test_unary.py::test_getitem [gw10] [ 94%] PASSED tests/test_unary.py::test_cluster[False] tests/test_unary.py::test_cluster_by[True] [gw2] [ 94%] PASSED tests/test_binary.py::test_nearest[None-True-False] tests/test_binary.py::test_nearest[None-True-same] [gw3] [ 94%] PASSED tests/test_binary.py::test_nearest[downstream-True-same] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw8] [ 94%] PASSED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw4] [ 95%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_binary.py::test_k_nearest[upstream-True-same-last] [gw0] [ 95%] PASSED tests/test_binary.py::test_intersect[opposite] [gw1] [ 95%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw5] [ 95%] PASSED tests/test_unary.py::test_cluster[True] tests/windows/test_windows.py::test_windows2 [gw5] [ 95%] PASSED tests/windows/test_windows.py::test_windows2 [gw7] [ 96%] PASSED tests/test_unary.py::test_cluster_by[False] tests/test_unary.py::test_merge_by[True] [gw9] [ 96%] PASSED tests/test_unary.py::test_windows [gw3] [ 96%] PASSED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw2] [ 96%] PASSED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw4] [ 96%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw1] [ 96%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw10] [ 97%] PASSED tests/test_unary.py::test_cluster_by[True] [gw3] [ 97%] PASSED tests/test_binary.py::test_nearest[downstream-False-False] [gw8] [ 97%] PASSED tests/test_binary.py::test_k_nearest_1_vs_nearest tests/test_change_chromosome_custom.py::test_change_chromosomes [gw8] [ 97%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw8] [ 97%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw8] [ 98%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_concat.py::test_concat_unstranded_stranded [gw8] [ 98%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw7] [ 98%] PASSED tests/test_unary.py::test_merge_by[True] [gw8] [ 98%] PASSED tests/test_count_overlaps.py::test_strand_vs_strand_same tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw2] [ 98%] PASSED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw8] [ 99%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw4] [ 99%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw2] [ 99%] PASSED tests/test_binary.py::test_nearest[None-False-False] tests/test_binary.py::test_nearest[None-False-same] [gw2] [ 99%] PASSED tests/test_binary.py::test_nearest[None-False-same] [gw4] [ 99%] PASSED tests/test_binary.py::test_k_nearest[None-False-opposite-last] tests/test_binary.py::test_k_nearest[None-False-same-last] [gw4] [100%] PASSED tests/test_binary.py::test_k_nearest[None-False-same-last] =================================== FAILURES =================================== ____________________ test_k_nearest[None-False-False-last] _____________________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:559: in test_k_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) tests/helpers.py:58: in assert_df_equal print("index equal", df1.index == df2.index) /usr/lib/python3/dist-packages/pandas/core/ops/common.py:76: in new_method return method(self, other) /usr/lib/python3/dist-packages/pandas/core/arraylike.py:40: in __eq__ return self._cmp_method(other, operator.eq) /usr/lib/python3/dist-packages/pandas/core/indexes/range.py:1070: in _cmp_method return super()._cmp_method(other, op) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = RangeIndex(start=0, stop=6, step=1) other = RangeIndex(start=0, stop=5, step=1), op = def _cmp_method(self, other, op): """ Wrapper used to dispatch comparison operations. """ if self.is_(other): # fastpath if op in {operator.eq, operator.le, operator.ge}: arr = np.ones(len(self), dtype=bool) if self._can_hold_na and not isinstance(self, ABCMultiIndex): # TODO: should set MultiIndex._can_hold_na = False? arr[self.isna()] = False return arr elif op is operator.ne: arr = np.zeros(len(self), dtype=bool) if self._can_hold_na and not isinstance(self, ABCMultiIndex): arr[self.isna()] = True return arr if isinstance(other, (np.ndarray, Index, ABCSeries, ExtensionArray)) and len( self ) != len(other): > raise ValueError("Lengths must match to compare") E ValueError: Lengths must match to compare E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3 | 4 | a | 0 | - | E | chr1 | 3 | 4 | a | 0 | - | E | chr1 | 3 | 6 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7 | 8 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7182 E /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7184 E /usr/lib/python3/dist-packages/pandas/core/indexes/range.py:1070 E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicHYexDQAgEAIPjSaWDuYsFk5s4R7+A4EDAVMLpH3eDYYpbgWKh+Qw1EjFqSb0LPi7/AM7') as a decorator on your test case /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7185: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpijng2oja/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijng2oja/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphpts8ury/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphpts8ury/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvt68isgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvt68isgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 2 chr1 2567198 2568737 - 184524 3 chr1 2567198 2568737 - 246165 4 chr1 2935424 2945424 + 115019 5 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 470969 | 477279 | a | 0 | ... | | chr1 | 470969 | 477279 | a | 0 | ... | | chr1 | 2935424 | 2945424 | a | 0 | ... | | chr1 | 2935424 | 2945424 | a | 0 | ... | | chr1 | 2567198 | 2568737 | a | 0 | ... | | chr1 | 2567198 | 2568737 | a | 0 | ... | | chr1 | 9646164 | 9653887 | a | 0 | ... | | chr1 | 9646164 | 9653887 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 4 chr1 2567198 2568737 - 184524 5 chr1 2567198 2568737 - 246165 2 chr1 2935424 2945424 + 115019 3 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 df2 Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 2 chr1 2567198 2568737 - 184524 3 chr1 2567198 2568737 - 246165 4 chr1 2935424 2945424 + 115019 5 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 Actual Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 2 chr1 2567198 2568737 - 184524 3 chr1 2567198 2568737 - 246165 4 chr1 2935424 2945424 + 115019 5 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 Expected Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 2 chr1 2567198 2568737 - 184524 3 chr1 2567198 2568737 - 246165 4 chr1 2935424 2945424 + 115019 5 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphq17iyon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphq17iyon/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmz7srey0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmz7srey0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1r5t2qxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1r5t2qxr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpma61y7w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma61y7w9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5526623 | 5530029 | a | 0 | ... | | chr1 | 5526623 | 5530029 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 df2 Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 Actual Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 Expected Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy2uym41w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2uym41w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_gcd7zwf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gcd7zwf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpykpw_59h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpykpw_59h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv595rge9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv595rge9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7a9rv3r4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7a9rv3r4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqm4gb4hz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqm4gb4hz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2888059 | a | 0 | ... | | chr1 | 2878713 | 2888059 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd45kslz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd45kslz1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2888059 | a | 0 | ... | | chr1 | 2878713 | 2888059 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq702mrgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq702mrgg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2878714 | a | 0 | ... | | chr1 | 2878713 | 2878714 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpopvy9kr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpopvy9kr6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2878714 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6rr3g079/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6rr3g079/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2878714 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpumjx0qw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumjx0qw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw6g_fr5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6g_fr5v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 2 chr1 5087609 5092865 - 184783 3 chr1 5087609 5092865 - 826946 4 chr1 6158835 6164150 - 231765 5 chr1 6158835 6164150 - 877248 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5087609 | 5087764 | a | 0 | ... | | chr1 | 5087609 | 5087764 | a | 0 | ... | | chr1 | 6158835 | 6164150 | a | 0 | ... | | chr1 | 6158835 | 6164150 | a | 0 | ... | | chr1 | 5087609 | 5092865 | a | 0 | ... | | chr1 | 5087609 | 5092865 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 4 chr1 5087609 5092865 - 184783 5 chr1 5087609 5092865 - 826946 2 chr1 6158835 6164150 - 231765 3 chr1 6158835 6164150 - 877248 df2 Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 2 chr1 5087609 5092865 - 184783 3 chr1 5087609 5092865 - 826946 4 chr1 6158835 6164150 - 231765 5 chr1 6158835 6164150 - 877248 Actual Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 2 chr1 5087609 5092865 - 184783 3 chr1 5087609 5092865 - 826946 4 chr1 6158835 6164150 - 231765 5 chr1 6158835 6164150 - 877248 Expected Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 2 chr1 5087609 5092865 - 184783 3 chr1 5087609 5092865 - 826946 4 chr1 6158835 6164150 - 231765 5 chr1 6158835 6164150 - 877248 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmjej5byd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjej5byd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppu4kf2kt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppu4kf2kt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6pn7z5am/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6pn7z5am/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5eu755ak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5eu755ak/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt6ccla5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6ccla5l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9hty0375/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hty0375/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpteehec2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpteehec2a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_gur1_gr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gur1_gr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx0neicsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0neicsr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7308093 | 7314471 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 df2 Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Actual Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Expected Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp05zya_jc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05zya_jc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7308093 | 7314471 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 df2 Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Actual Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Expected Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2g8lt36f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2g8lt36f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9903 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 df2 Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 Actual Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 Expected Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6nwodw6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6nwodw6v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 4 chr9 3128776 3131715 + 612750 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9903 | a | 0 | ... | | chr9 | 3128776 | 3131715 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 1 chr9 3128776 3131715 + 612750 df2 Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 4 chr9 3128776 3131715 + 612750 Actual Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 1 chr9 3128776 3131715 + 612750 Expected Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 1 chr9 3128776 3131715 + 612750 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpls12768j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpls12768j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 4 chr9 9236 9237 + 3735228 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 9902 | a | 0 | ... | | chr9 | 9236 | 9237 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 1 chr9 9236 9237 + 3735228 df2 Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 4 chr9 9236 9237 + 3735228 Actual Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 1 chr9 9236 9237 + 3735228 Expected Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 1 chr9 9236 9237 + 3735228 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4xclw7uz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xclw7uz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1dfkyxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1dfkyxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp30sua0m1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp30sua0m1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiicjzclu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiicjzclu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpohf2itz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohf2itz6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_t_5f1af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_t_5f1af/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpww3rh6e4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpww3rh6e4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzxr9_jqi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxr9_jqi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqxycckhv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqxycckhv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtxnb2c5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtxnb2c5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbc0gqz5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc0gqz5v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpltjpy14m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpltjpy14m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb20qmbva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb20qmbva/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9564930 | 9565690 | a | 0 | ... | | chr1 | 3756769 | 3758615 | a | 0 | ... | | chr1 | 5631250 | 5633096 | a | 0 | ... | | chr1 | 6631754 | 6633600 | a | 0 | ... | | chr1 | 3893027 | 3894873 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3756769 3758615 + 6191337 4 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 0 chr1 9564930 9565690 + 384262 df2 Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Actual Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Expected Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa9uy_kba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9uy_kba/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9564930 | 9565690 | a | 0 | ... | | chr1 | 3756769 | 3758615 | a | 0 | ... | | chr1 | 5631250 | 5633096 | a | 0 | ... | | chr1 | 6631754 | 6633600 | a | 0 | ... | | chr1 | 3893027 | 3894873 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3756769 3758615 + 6191337 4 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 0 chr1 9564930 9565690 + 384262 df2 Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Actual Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Expected Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_g5vqum0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g5vqum0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2b4gvcw6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2b4gvcw6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnogqcm81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnogqcm81/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3wiry99d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wiry99d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp47mlkkwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47mlkkwh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppfyli0wh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfyli0wh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2er6p2xz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2er6p2xz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph2cv5jro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2cv5jro/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdcuio71z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcuio71z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf9y_0_3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9y_0_3p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8zln4j0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8zln4j0u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2uwq50zy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uwq50zy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpea9k0skl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea9k0skl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa09g_5tr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa09g_5tr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmxrva_1q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxrva_1q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsshayx4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsshayx4a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr3_y167c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3_y167c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprabamv9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprabamv9n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6529846 | 6532809 | a | 0 | ... | | chr1 | 6529846 | 6532809 | a | 0 | ... | | chr1 | 7309406 | 7311515 | a | 0 | ... | | chr1 | 7309406 | 7311515 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 df2 Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 Actual Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 Expected Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfwicx8xf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfwicx8xf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 2 chr1 2292934 2294596 + 14750 3 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 6 chr1 2309345 2316283 - 9899 7 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 12 chr1 9286212 9294610 + 2909283 13 chr1 9286212 9294610 + 4898709 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 6 chr1 2292934 2294596 + 14750 7 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 12 chr1 2309345 2316283 - 9899 13 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 2 chr1 9286212 9294610 + 2909283 3 chr1 9286212 9294610 + 4898709 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 2 chr1 2292934 2294596 + 14750 3 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 6 chr1 2309345 2316283 - 9899 7 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 12 chr1 9286212 9294610 + 2909283 13 chr1 9286212 9294610 + 4898709 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 2 chr1 2292934 2294596 + 14750 3 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 6 chr1 2309345 2316283 - 9899 7 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 12 chr1 9286212 9294610 + 2909283 13 chr1 9286212 9294610 + 4898709 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 2 chr1 2292934 2294596 + 14750 3 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 6 chr1 2309345 2316283 - 9899 7 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 12 chr1 9286212 9294610 + 2909283 13 chr1 9286212 9294610 + 4898709 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2yiyuej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2yiyuej/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 2292934 | 2299447 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr3 | 6851060 | 6853898 | a | 0 | ... | | chr5 | 2751097 | 2751853 | a | 0 | ... | | chr6 | 2292934 | 2297051 | a | 0 | ... | | chr20 | 8824422 | 8832590 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 5 chr1 2292934 2294596 + 1207768 6 chr1 2292934 2294596 + 1216717 15 chr6 2292934 2297051 + 1207768 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 11 chr1 2309345 2316283 - 1224179 12 chr1 2309345 2316283 - 1233128 14 chr5 2751097 2751853 - 1674887 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 13 chr3 6851060 6853898 - 6785523 16 chr20 8824422 8832590 + 8758881 1 chr1 9286212 9294610 + 8201046 2 chr1 9286212 9294610 + 8209995 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 16 chr6 2292934 2297051 + 1207768 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 15 chr5 2751097 2751853 - 1674887 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 14 chr3 6851060 6853898 - 6785523 13 chr20 8824422 8832590 + 8758881 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkvleh0l3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvleh0l3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 2292934 | 2299447 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr3 | 6851060 | 6853898 | a | 0 | ... | | chr5 | 2751097 | 2751853 | a | 0 | ... | | chr6 | 2292934 | 2297051 | a | 0 | ... | | chr20 | 8824422 | 8832590 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 5 chr1 2292934 2294596 + 1207768 6 chr1 2292934 2294596 + 1216717 15 chr6 2292934 2297051 + 1207768 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 11 chr1 2309345 2316283 - 1224179 12 chr1 2309345 2316283 - 1233128 14 chr5 2751097 2751853 - 1674887 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 13 chr3 6851060 6853898 - 6785523 16 chr20 8824422 8832590 + 8758881 1 chr1 9286212 9294610 + 8201046 2 chr1 9286212 9294610 + 8209995 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 16 chr6 2292934 2297051 + 1207768 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 15 chr5 2751097 2751853 - 1674887 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 14 chr3 6851060 6853898 - 6785523 13 chr20 8824422 8832590 + 8758881 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphblr3p_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphblr3p_7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 2 chr1 2292934 2294596 + 2227397 3 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 6 chr1 2309345 2316283 - 2243808 7 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 12 chr1 9286212 9294610 + 9220675 13 chr1 9286212 9294610 + 9286193 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 6 chr1 2292934 2294596 + 2227397 7 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 12 chr1 2309345 2316283 - 2243808 13 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 2 chr1 9286212 9294610 + 9220675 3 chr1 9286212 9294610 + 9286193 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 2 chr1 2292934 2294596 + 2227397 3 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 6 chr1 2309345 2316283 - 2243808 7 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 12 chr1 9286212 9294610 + 9220675 13 chr1 9286212 9294610 + 9286193 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 2 chr1 2292934 2294596 + 2227397 3 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 6 chr1 2309345 2316283 - 2243808 7 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 12 chr1 9286212 9294610 + 9220675 13 chr1 9286212 9294610 + 9286193 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 2 chr1 2292934 2294596 + 2227397 3 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 6 chr1 2309345 2316283 - 2243808 7 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 12 chr1 9286212 9294610 + 9220675 13 chr1 9286212 9294610 + 9286193 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp64qe5ca6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64qe5ca6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 2 chr1 2292934 2294596 + 2227379 3 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 6 chr1 2309345 2316283 - 2243790 7 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 12 chr1 9286212 9294610 + 9220657 13 chr1 9286212 9294610 + 9220675 14 chr20 8824422 8832590 + 8758867 15 chr3 6851060 6853898 - 6785505 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 6 chr1 2292934 2294596 + 2227379 7 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 12 chr1 2309345 2316283 - 2243790 13 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 14 chr3 6851060 6853898 - 6785505 15 chr20 8824422 8832590 + 8758867 2 chr1 9286212 9294610 + 9220657 3 chr1 9286212 9294610 + 9220675 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 2 chr1 2292934 2294596 + 2227379 3 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 6 chr1 2309345 2316283 - 2243790 7 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 15 chr3 6851060 6853898 - 6785505 14 chr20 8824422 8832590 + 8758867 12 chr1 9286212 9294610 + 9220657 13 chr1 9286212 9294610 + 9220675 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 2 chr1 2292934 2294596 + 2227379 3 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 6 chr1 2309345 2316283 - 2243790 7 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 12 chr1 9286212 9294610 + 9220657 13 chr1 9286212 9294610 + 9220675 14 chr20 8824422 8832590 + 8758867 15 chr3 6851060 6853898 - 6785505 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 2 chr1 2292934 2294596 + 2227379 3 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 6 chr1 2309345 2316283 - 2243790 7 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 12 chr1 9286212 9294610 + 9220657 13 chr1 9286212 9294610 + 9220675 14 chr20 8824422 8832590 + 8758867 15 chr3 6851060 6853898 - 6785505 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgr67are2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgr67are2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 1 chr1 1076210 1076215 + 1076200 2 chr1 1076210 1076215 - 1010673 3 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 6 chr1 1076210 1085167 - 1010673 7 chr1 1076210 1085167 - 1076200 8 chr1 1076210 1085167 - 1010673 9 chr1 1076210 1085167 - 1076200 10 chr1 1076210 1085167 - 1010673 11 chr1 1076210 1085167 - 1076200 12 chr2 1076210 1076215 - 1010673 13 chr2 1076210 1085231 - 1010673 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1076215 | a | 0 | ... | | chr1 | 1076210 | 1076215 | a | 0 | ... | | chr1 | 1076210 | 1085167 | a | 0 | ... | | chr1 | 1076210 | 1085167 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1076210 | 1076215 | a | 0 | ... | | chr1 | 1076210 | 1076215 | a | 0 | ... | | chr1 | 1076210 | 1085167 | a | 0 | ... | | chr1 | 1076210 | 1085167 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 8 chr1 1076210 1076215 - 1010673 12 chr2 1076210 1076215 - 1010673 1 chr1 1076210 1076215 + 1076200 9 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 2 chr1 1076210 1085167 - 1010673 6 chr1 1076210 1085167 - 1010673 10 chr1 1076210 1085167 - 1010673 3 chr1 1076210 1085167 - 1076200 7 chr1 1076210 1085167 - 1076200 11 chr1 1076210 1085167 - 1076200 13 chr2 1076210 1085231 - 1010673 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 2 chr1 1076210 1076215 - 1010673 12 chr2 1076210 1076215 - 1010673 1 chr1 1076210 1076215 + 1076200 3 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 6 chr1 1076210 1085167 - 1010673 8 chr1 1076210 1085167 - 1010673 10 chr1 1076210 1085167 - 1010673 7 chr1 1076210 1085167 - 1076200 9 chr1 1076210 1085167 - 1076200 11 chr1 1076210 1085167 - 1076200 13 chr2 1076210 1085231 - 1010673 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 1 chr1 1076210 1076215 + 1076200 2 chr1 1076210 1076215 - 1010673 3 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 6 chr1 1076210 1085167 - 1010673 7 chr1 1076210 1085167 - 1010673 8 chr1 1076210 1085167 - 1010673 9 chr1 1076210 1085167 - 1076200 10 chr1 1076210 1085167 - 1076200 11 chr1 1076210 1085167 - 1076200 12 chr2 1076210 1076215 - 1010673 13 chr2 1076210 1085231 - 1010673 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 1 chr1 1076210 1076215 + 1076200 2 chr1 1076210 1076215 - 1010673 3 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 6 chr1 1076210 1085167 - 1010673 7 chr1 1076210 1085167 - 1010673 8 chr1 1076210 1085167 - 1010673 9 chr1 1076210 1085167 - 1076200 10 chr1 1076210 1085167 - 1076200 11 chr1 1076210 1085167 - 1076200 12 chr2 1076210 1076215 - 1010673 13 chr2 1076210 1085231 - 1010673 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnokqbaad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnokqbaad/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 170894 178569 + 1416759 1 chr1 2805781 2814560 + 1209787 2 chr1 2813180 2821374 + 1217186 3 chr1 3891627 3891795 + 2295633 4 chr1 5047825 5057824 + 3451831 5 chr1 8366071 8373036 + 6770077 6 chr1 9011544 9016707 + 7415550 7 chr1 9328478 9334107 + 7732484 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | chr1 | 3891627 | 3891795 | a | 0 | ... | | chr1 | 5047825 | 5057824 | a | 0 | ... | | chr1 | 8366071 | 8373036 | a | 0 | ... | | chr1 | 2805781 | 2814560 | a | 0 | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chr1 170894 178569 + 1416759 5 chr1 2805781 2814560 + 1209787 6 chr1 2813180 2821374 + 1217186 2 chr1 3891627 3891795 + 2295633 3 chr1 5047825 5057824 + 3451831 4 chr1 8366071 8373036 + 6770077 0 chr1 9011544 9016707 + 7415550 1 chr1 9328478 9334107 + 7732484 df2 Chromosome Start End Strand Distance 0 chr1 170894 178569 + 1416759 1 chr1 2805781 2814560 + 1209787 2 chr1 2813180 2821374 + 1217186 3 chr1 3891627 3891795 + 2295633 4 chr1 5047825 5057824 + 3451831 5 chr1 8366071 8373036 + 6770077 6 chr1 9011544 9016707 + 7415550 7 chr1 9328478 9334107 + 7732484 Actual Chromosome Start End Strand Distance 0 chr1 170894 178569 + 1416759 1 chr1 2805781 2814560 + 1209787 2 chr1 2813180 2821374 + 1217186 3 chr1 3891627 3891795 + 2295633 4 chr1 5047825 5057824 + 3451831 5 chr1 8366071 8373036 + 6770077 6 chr1 9011544 9016707 + 7415550 7 chr1 9328478 9334107 + 7732484 Expected Chromosome Start End Strand Distance 0 chr1 170894 178569 + 1416759 1 chr1 2805781 2814560 + 1209787 2 chr1 2813180 2821374 + 1217186 3 chr1 3891627 3891795 + 2295633 4 chr1 5047825 5057824 + 3451831 5 chr1 8366071 8373036 + 6770077 6 chr1 9011544 9016707 + 7415550 7 chr1 9328478 9334107 + 7732484 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9jnnl5q4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jnnl5q4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 311772 15 chr1 9328478 9334107 + 955443 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr1 170894 178569 + 2627213 15 chr1 170894 178569 + 2634612 10 chr1 2805781 2814560 + 1077068 11 chr1 2805781 2814560 + 2233266 12 chr1 2813180 2821374 + 1070254 13 chr1 2813180 2821374 + 2226452 4 chr1 3891627 3891795 + 1070254 5 chr1 3891627 3891795 + 1077068 6 chr1 5047825 5057824 + 1156031 7 chr1 5047825 5057824 + 2226452 8 chr1 8366071 8373036 + 638509 9 chr1 8366071 8373036 + 955443 0 chr1 9011544 9016707 + 311772 1 chr1 9011544 9016707 + 638509 2 chr1 9328478 9334107 + 311772 3 chr1 9328478 9334107 + 955443 df2 Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 311772 15 chr1 9328478 9334107 + 955443 Actual Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 311772 15 chr1 9328478 9334107 + 955443 Expected Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 311772 15 chr1 9328478 9334107 + 955443 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1awll_f6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1awll_f6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 316933 15 chr1 9328478 9334107 + 955443 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr1 170894 178569 + 2627213 15 chr1 170894 178569 + 2634612 10 chr1 2805781 2814560 + 1077068 11 chr1 2805781 2814560 + 2233266 12 chr1 2813180 2821374 + 1070254 13 chr1 2813180 2821374 + 2226452 4 chr1 3891627 3891795 + 1070254 5 chr1 3891627 3891795 + 1077068 6 chr1 5047825 5057824 + 1156031 7 chr1 5047825 5057824 + 2226452 8 chr1 8366071 8373036 + 638509 9 chr1 8366071 8373036 + 955443 0 chr1 9011544 9016707 + 311772 1 chr1 9011544 9016707 + 638509 2 chr1 9328478 9334107 + 316933 3 chr1 9328478 9334107 + 955443 df2 Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 316933 15 chr1 9328478 9334107 + 955443 Actual Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 316933 15 chr1 9328478 9334107 + 955443 Expected Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 316933 15 chr1 9328478 9334107 + 955443 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplwm47ss3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwm47ss3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpivjvkf3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivjvkf3d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 78 4 chr1 1 2 - 9 5 chr1 1 2 - 78 6 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 8 chr1 1 3673 - 61865 9 chr1 1 5122 - 60416 10 chr1 1 669 - 64869 11 chr1 1 9854 - 55684 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 9854 | a | 0 | ... | | chr1 | 1 | 2435 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 5122 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 669 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 9 5 chr1 1 2 - 9 9 chr1 1 2 - 9 1 chr1 1 2 + 78 6 chr1 1 2 - 78 10 chr1 1 2 - 78 11 chr1 1 669 - 64869 3 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 4 chr1 1 3673 - 61865 8 chr1 1 5122 - 60416 2 chr1 1 9854 - 55684 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 9 2 chr1 1 2 - 9 4 chr1 1 2 - 9 1 chr1 1 2 + 78 3 chr1 1 2 - 78 5 chr1 1 2 - 78 10 chr1 1 669 - 64869 6 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 8 chr1 1 3673 - 61865 9 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 9 4 chr1 1 2 - 78 5 chr1 1 2 - 78 6 chr1 1 669 - 64869 7 chr1 1 2435 - 63103 8 chr1 1 3336 - 62202 9 chr1 1 3673 - 61865 10 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 9 4 chr1 1 2 - 78 5 chr1 1 2 - 78 6 chr1 1 669 - 64869 7 chr1 1 2435 - 63103 8 chr1 1 3336 - 62202 9 chr1 1 3673 - 61865 10 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsbdrzmz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbdrzmz5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 78 4 chr1 1 2 - 9 5 chr1 1 2 - 78 6 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 8 chr1 1 3673 - 61865 9 chr1 1 5122 - 60416 10 chr1 1 669 - 64869 11 chr1 1 9854 - 55684 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 9854 | a | 0 | ... | | chr1 | 1 | 2435 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 5122 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 669 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 9 5 chr1 1 2 - 9 9 chr1 1 2 - 9 1 chr1 1 2 + 78 6 chr1 1 2 - 78 10 chr1 1 2 - 78 11 chr1 1 669 - 64869 3 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 4 chr1 1 3673 - 61865 8 chr1 1 5122 - 60416 2 chr1 1 9854 - 55684 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 9 2 chr1 1 2 - 9 4 chr1 1 2 - 9 1 chr1 1 2 + 78 3 chr1 1 2 - 78 5 chr1 1 2 - 78 10 chr1 1 669 - 64869 6 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 8 chr1 1 3673 - 61865 9 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 9 4 chr1 1 2 - 78 5 chr1 1 2 - 78 6 chr1 1 669 - 64869 7 chr1 1 2435 - 63103 8 chr1 1 3336 - 62202 9 chr1 1 3673 - 61865 10 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 9 4 chr1 1 2 - 78 5 chr1 1 2 - 78 6 chr1 1 669 - 64869 7 chr1 1 2435 - 63103 8 chr1 1 3336 - 62202 9 chr1 1 3673 - 61865 10 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmf7ybvgk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmf7ybvgk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 8558 - 56980 1 chr1 10 47 - 33 2 chr1 10 47 - 65491 3 chr1 79 336 - 33 4 chr1 79 336 - 65202 5 chr1 79 336 - 33 6 chr1 79 336 - 65202 7 chr1 79 336 - 33 8 chr1 79 336 - 65202 9 chr1 79 336 - 33 10 chr1 79 336 - 65202 11 chr1 79 85 - 33 12 chr1 79 85 - 65453 13 chr1 65537 65794 - 56980 14 chr1 65537 65794 - 65202 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10 | 47 | a | 0 | ... | | chr1 | 10 | 47 | a | 0 | ... | | chr1 | 1 | 8558 | a | 0 | ... | | chr1 | 79 | 336 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 79 | 336 | a | 0 | ... | | chr1 | 79 | 336 | a | 0 | ... | | chr1 | 79 | 336 | a | 0 | ... | | chr1 | 79 | 336 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 8558 - 56980 0 chr1 10 47 - 33 1 chr1 10 47 - 65491 9 chr1 79 85 - 33 10 chr1 79 85 - 65453 3 chr1 79 336 - 33 7 chr1 79 336 - 33 11 chr1 79 336 - 33 13 chr1 79 336 - 33 4 chr1 79 336 - 65202 8 chr1 79 336 - 65202 12 chr1 79 336 - 65202 14 chr1 79 336 - 65202 5 chr1 65537 65794 - 56980 6 chr1 65537 65794 - 65202 df2 Chromosome Start End Strand Distance 0 chr1 1 8558 - 56980 1 chr1 10 47 - 33 2 chr1 10 47 - 65491 11 chr1 79 85 - 33 12 chr1 79 85 - 65453 3 chr1 79 336 - 33 5 chr1 79 336 - 33 7 chr1 79 336 - 33 9 chr1 79 336 - 33 4 chr1 79 336 - 65202 6 chr1 79 336 - 65202 8 chr1 79 336 - 65202 10 chr1 79 336 - 65202 13 chr1 65537 65794 - 56980 14 chr1 65537 65794 - 65202 Actual Chromosome Start End Strand Distance 0 chr1 1 8558 - 56980 1 chr1 10 47 - 33 2 chr1 10 47 - 65491 3 chr1 79 85 - 33 4 chr1 79 85 - 65453 5 chr1 79 336 - 33 6 chr1 79 336 - 33 7 chr1 79 336 - 33 8 chr1 79 336 - 33 9 chr1 79 336 - 65202 10 chr1 79 336 - 65202 11 chr1 79 336 - 65202 12 chr1 79 336 - 65202 13 chr1 65537 65794 - 56980 14 chr1 65537 65794 - 65202 Expected Chromosome Start End Strand Distance 0 chr1 1 8558 - 56980 1 chr1 10 47 - 33 2 chr1 10 47 - 65491 3 chr1 79 85 - 33 4 chr1 79 85 - 65453 5 chr1 79 336 - 33 6 chr1 79 336 - 33 7 chr1 79 336 - 33 8 chr1 79 336 - 33 9 chr1 79 336 - 65202 10 chr1 79 336 - 65202 11 chr1 79 336 - 65202 12 chr1 79 336 - 65202 13 chr1 65537 65794 - 56980 14 chr1 65537 65794 - 65202 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=15, step=1) index equal [ True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplz14tyeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplz14tyeh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpja764doa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja764doa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2je2aeah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2je2aeah/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy7q4rta2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7q4rta2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqd2q9kou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd2q9kou/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd7wn65c2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7wn65c2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_mgn8bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_mgn8bi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 4783661 1 chr1 7826699 7826700 + 7761162 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7826699 | 7826700 | a | 0 | ... | | chr1 | 4849198 | 4856651 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4849198 4856651 + 4783661 0 chr1 7826699 7826700 + 7761162 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 4783661 1 chr1 7826699 7826700 + 7761162 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 4783661 1 chr1 7826699 7826700 + 7761162 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 4783661 1 chr1 7826699 7826700 + 7761162 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb1m32uvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1m32uvq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 6 chr12 5191349 5197809 + 4082195 7 chr15 221755 224156 - 86234 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 1550927 | 1560604 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr12 | 5191349 | 5197809 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr15 221755 224156 - 86234 2 chr1 1550927 1560604 - 6265203 5 chr12 5191349 5197809 + 4082195 3 chr1 7078483 7087002 - 738805 4 chr1 7148878 7151354 - 674453 1 chr1 7149314 7153375 - 672432 0 chr1 8264194 8264945 - 434118 df2 Chromosome Start End Strand Distance 7 chr15 221755 224156 - 86234 0 chr1 1550927 1560604 - 6265203 6 chr12 5191349 5197809 + 4082195 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph6_9vnlg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6_9vnlg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 6 chr12 5191349 5197809 + 4082195 7 chr15 221755 224156 - 86234 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 1550927 | 1560604 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr12 | 5191349 | 5197809 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr15 221755 224156 - 86234 2 chr1 1550927 1560604 - 6265203 5 chr12 5191349 5197809 + 4082195 3 chr1 7078483 7087002 - 738805 4 chr1 7148878 7151354 - 674453 1 chr1 7149314 7153375 - 672432 0 chr1 8264194 8264945 - 434118 df2 Chromosome Start End Strand Distance 7 chr15 221755 224156 - 86234 0 chr1 1550927 1560604 - 6265203 6 chr12 5191349 5197809 + 4082195 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkved3xh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkved3xh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 6 chr12 5191349 5197809 + 4082195 7 chr15 221755 224156 - 86234 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 1550927 | 1560604 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr12 | 5191349 | 5197809 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr15 221755 224156 - 86234 2 chr1 1550927 1560604 - 6265203 5 chr12 5191349 5197809 + 4082195 3 chr1 7078483 7087002 - 738805 4 chr1 7148878 7151354 - 674453 1 chr1 7149314 7153375 - 672432 0 chr1 8264194 8264945 - 434118 df2 Chromosome Start End Strand Distance 7 chr15 221755 224156 - 86234 0 chr1 1550927 1560604 - 6265203 6 chr12 5191349 5197809 + 4082195 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz85mqga0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz85mqga0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 5517880 1 chr1 1550927 1560604 - 5588275 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 61877 5 chr1 7148878 7151354 - 1112841 6 chr1 7149314 7153375 - 62313 7 chr1 7149314 7153375 - 1110820 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1550927 1560604 - 5517880 5 chr1 1550927 1560604 - 5588275 6 chr1 7078483 7087002 - 61877 7 chr1 7078483 7087002 - 62313 8 chr1 7148878 7151354 - 61877 9 chr1 7148878 7151354 - 1112841 2 chr1 7149314 7153375 - 62313 3 chr1 7149314 7153375 - 1110820 0 chr1 8264194 8264945 - 1110820 1 chr1 8264194 8264945 - 1112841 df2 Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 5517880 1 chr1 1550927 1560604 - 5588275 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 61877 5 chr1 7148878 7151354 - 1112841 6 chr1 7149314 7153375 - 62313 7 chr1 7149314 7153375 - 1110820 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 5517880 1 chr1 1550927 1560604 - 5588275 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 61877 5 chr1 7148878 7151354 - 1112841 6 chr1 7149314 7153375 - 62313 7 chr1 7149314 7153375 - 1110820 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 5517880 1 chr1 1550927 1560604 - 5588275 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 61877 5 chr1 7148878 7151354 - 1112841 6 chr1 7149314 7153375 - 62313 7 chr1 7149314 7153375 - 1110820 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa20em6tr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa20em6tr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1542404 1 chr1 1550927 1560604 - 1550176 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 5588275 5 chr1 7148878 7151354 - 7140355 6 chr1 7149314 7153375 - 5588711 7 chr1 7149314 7153375 - 7140791 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1550927 1560604 - 1542404 5 chr1 1550927 1560604 - 1550176 6 chr1 7078483 7087002 - 61877 7 chr1 7078483 7087002 - 62313 8 chr1 7148878 7151354 - 5588275 9 chr1 7148878 7151354 - 7140355 2 chr1 7149314 7153375 - 5588711 3 chr1 7149314 7153375 - 7140791 0 chr1 8264194 8264945 - 1110820 1 chr1 8264194 8264945 - 1112841 df2 Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1542404 1 chr1 1550927 1560604 - 1550176 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 5588275 5 chr1 7148878 7151354 - 7140355 6 chr1 7149314 7153375 - 5588711 7 chr1 7149314 7153375 - 7140791 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1542404 1 chr1 1550927 1560604 - 1550176 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 5588275 5 chr1 7148878 7151354 - 7140355 6 chr1 7149314 7153375 - 5588711 7 chr1 7149314 7153375 - 7140791 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1542404 1 chr1 1550927 1560604 - 1550176 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 5588275 5 chr1 7148878 7151354 - 7140355 6 chr1 7149314 7153375 - 5588711 7 chr1 7149314 7153375 - 7140791 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm8tin5a8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8tin5a8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1531574 1 chr1 1550927 1560604 - 1533890 2 chr1 7078483 7087002 - 7059130 3 chr1 7078483 7087002 - 7061446 4 chr1 7148878 7151354 - 7129525 5 chr1 7148878 7151354 - 7131841 6 chr1 7149314 7153375 - 7129961 7 chr1 7149314 7153375 - 7132277 8 chr1 8264194 8264945 - 8244841 9 chr1 8264194 8264945 - 8247157 10 chr11 7674207 7674929 + 7672764 12 chr15 221755 224156 - 216954 14 chr5 9877776 9883670 - 9865989 15 chrX 6801859 6811661 + 6782256 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr5 | 9877776 | 9883670 | a | 0 | ... | | chr11 | 7674207 | 7674929 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | | chrX | 6801859 | 6811661 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 12 chr15 221755 224156 - 216954 4 chr1 1550927 1560604 - 1531574 5 chr1 1550927 1560604 - 1533890 13 chrX 6801859 6811661 + 6782256 6 chr1 7078483 7087002 - 7059130 7 chr1 7078483 7087002 - 7061446 8 chr1 7148878 7151354 - 7129525 9 chr1 7148878 7151354 - 7131841 2 chr1 7149314 7153375 - 7129961 3 chr1 7149314 7153375 - 7132277 11 chr11 7674207 7674929 + 7672764 0 chr1 8264194 8264945 - 8244841 1 chr1 8264194 8264945 - 8247157 10 chr5 9877776 9883670 - 9865989 df2 Chromosome Start End Strand Distance 12 chr15 221755 224156 - 216954 0 chr1 1550927 1560604 - 1531574 1 chr1 1550927 1560604 - 1533890 15 chrX 6801859 6811661 + 6782256 2 chr1 7078483 7087002 - 7059130 3 chr1 7078483 7087002 - 7061446 4 chr1 7148878 7151354 - 7129525 5 chr1 7148878 7151354 - 7131841 6 chr1 7149314 7153375 - 7129961 7 chr1 7149314 7153375 - 7132277 10 chr11 7674207 7674929 + 7672764 8 chr1 8264194 8264945 - 8244841 9 chr1 8264194 8264945 - 8247157 14 chr5 9877776 9883670 - 9865989 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1531574 1 chr1 1550927 1560604 - 1533890 2 chr1 7078483 7087002 - 7059130 3 chr1 7078483 7087002 - 7061446 4 chr1 7148878 7151354 - 7129525 5 chr1 7148878 7151354 - 7131841 6 chr1 7149314 7153375 - 7129961 7 chr1 7149314 7153375 - 7132277 8 chr1 8264194 8264945 - 8244841 9 chr1 8264194 8264945 - 8247157 10 chr11 7674207 7674929 + 7672764 11 chr15 221755 224156 - 216954 12 chr5 9877776 9883670 - 9865989 13 chrX 6801859 6811661 + 6782256 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1531574 1 chr1 1550927 1560604 - 1533890 2 chr1 7078483 7087002 - 7059130 3 chr1 7078483 7087002 - 7061446 4 chr1 7148878 7151354 - 7129525 5 chr1 7148878 7151354 - 7131841 6 chr1 7149314 7153375 - 7129961 7 chr1 7149314 7153375 - 7132277 8 chr1 8264194 8264945 - 8244841 9 chr1 8264194 8264945 - 8247157 10 chr11 7674207 7674929 + 7672764 11 chr15 221755 224156 - 216954 12 chr5 9877776 9883670 - 9865989 13 chrX 6801859 6811661 + 6782256 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgnut2t7n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnut2t7n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1540500 1 chr1 1550927 1560604 - 1541658 2 chr1 7078483 7087002 - 7068056 3 chr1 7078483 7087002 - 7069214 4 chr1 7148878 7151354 - 7138451 5 chr1 7148878 7151354 - 7139609 6 chr1 7149314 7153375 - 7138887 7 chr1 7149314 7153375 - 7140045 8 chr1 8264194 8264945 - 8253767 9 chr1 8264194 8264945 - 8254925 10 chr11 7674207 7674929 + 7672735 12 chr15 221755 224156 - 218604 13 chr3 1 723 + 29 14 chr5 9877776 9883670 - 9871132 15 chrX 6801859 6811661 + 6791307 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr5 | 9877776 | 9883670 | a | 0 | ... | | chr11 | 7674207 | 7674929 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | | chrX | 6801859 | 6811661 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr3 1 723 + 29 13 chr15 221755 224156 - 218604 4 chr1 1550927 1560604 - 1540500 5 chr1 1550927 1560604 - 1541658 14 chrX 6801859 6811661 + 6791307 6 chr1 7078483 7087002 - 7068056 7 chr1 7078483 7087002 - 7069214 8 chr1 7148878 7151354 - 7138451 9 chr1 7148878 7151354 - 7139609 2 chr1 7149314 7153375 - 7138887 3 chr1 7149314 7153375 - 7140045 12 chr11 7674207 7674929 + 7672735 0 chr1 8264194 8264945 - 8253767 1 chr1 8264194 8264945 - 8254925 11 chr5 9877776 9883670 - 9871132 df2 Chromosome Start End Strand Distance 13 chr3 1 723 + 29 12 chr15 221755 224156 - 218604 0 chr1 1550927 1560604 - 1540500 1 chr1 1550927 1560604 - 1541658 15 chrX 6801859 6811661 + 6791307 2 chr1 7078483 7087002 - 7068056 3 chr1 7078483 7087002 - 7069214 4 chr1 7148878 7151354 - 7138451 5 chr1 7148878 7151354 - 7139609 6 chr1 7149314 7153375 - 7138887 7 chr1 7149314 7153375 - 7140045 10 chr11 7674207 7674929 + 7672735 8 chr1 8264194 8264945 - 8253767 9 chr1 8264194 8264945 - 8254925 14 chr5 9877776 9883670 - 9871132 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1540500 1 chr1 1550927 1560604 - 1541658 2 chr1 7078483 7087002 - 7068056 3 chr1 7078483 7087002 - 7069214 4 chr1 7148878 7151354 - 7138451 5 chr1 7148878 7151354 - 7139609 6 chr1 7149314 7153375 - 7138887 7 chr1 7149314 7153375 - 7140045 8 chr1 8264194 8264945 - 8253767 9 chr1 8264194 8264945 - 8254925 10 chr11 7674207 7674929 + 7672735 11 chr15 221755 224156 - 218604 12 chr3 1 723 + 29 13 chr5 9877776 9883670 - 9871132 14 chrX 6801859 6811661 + 6791307 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1540500 1 chr1 1550927 1560604 - 1541658 2 chr1 7078483 7087002 - 7068056 3 chr1 7078483 7087002 - 7069214 4 chr1 7148878 7151354 - 7138451 5 chr1 7148878 7151354 - 7139609 6 chr1 7149314 7153375 - 7138887 7 chr1 7149314 7153375 - 7140045 8 chr1 8264194 8264945 - 8253767 9 chr1 8264194 8264945 - 8254925 10 chr11 7674207 7674929 + 7672735 11 chr15 221755 224156 - 218604 12 chr3 1 723 + 29 13 chr5 9877776 9883670 - 9871132 14 chrX 6801859 6811661 + 6791307 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=15, step=1) index equal [ True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6cff2wvn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cff2wvn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4456359 | 4456634 | a | 0 | ... | | chr1 | 8017027 | 8017372 | a | 0 | ... | | chr1 | 7501587 | 7508273 | a | 0 | ... | | chr1 | 10000000 | 10002710 | a | 0 | ... | | chr1 | 10000000 | 10009559 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 2 chr1 7501587 7508273 + 4470141 1 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_97pt58i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_97pt58i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4456359 | 4456634 | a | 0 | ... | | chr1 | 8017027 | 8017372 | a | 0 | ... | | chr1 | 7501587 | 7508273 | a | 0 | ... | | chr1 | 10000000 | 10002710 | a | 0 | ... | | chr1 | 10000000 | 10009559 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 2 chr1 7501587 7508273 + 4470141 1 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8jmo_oki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jmo_oki/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390770 1 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 3 chr1 10000000 10000004 - 9934411 4 chr1 10000000 10000257 + 9934411 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 4456359 | 4456363 | a | 0 | ... | | chr1 | 8017027 | 8017028 | a | 0 | ... | | chr1 | 7501587 | 7501591 | a | 0 | ... | | chr1 | 10000000 | 10000004 | a | 0 | ... | | chr2 | 5920462 | 5920466 | a | 0 | ... | | chr2 | 5920462 | 5920466 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4456359 4456363 - 4390770 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 3 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 4 chr1 10000000 10000004 - 9934411 0 chr1 10000000 10000257 + 9934411 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390770 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 1 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 3 chr1 10000000 10000004 - 9934411 4 chr1 10000000 10000257 + 9934411 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390770 1 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 3 chr1 10000000 10000004 - 9934411 4 chr1 10000000 10000257 + 9934411 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390770 1 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 3 chr1 10000000 10000004 - 9934411 4 chr1 10000000 10000257 + 9934411 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzk81v9o9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzk81v9o9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390822 1 chr1 4456359 4456363 - 4456357 2 chr1 7501587 7501591 - 7436050 3 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 6 chr1 10000000 10000004 - 9934463 7 chr1 10000000 10000004 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 4456359 | 4456363 | a | 0 | ... | | chr1 | 4456359 | 4456363 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7501587 | 7501591 | a | 0 | ... | | chr1 | 7501587 | 7501591 | a | 0 | ... | | chr1 | 10000000 | 10000004 | a | 0 | ... | | chr1 | 10000000 | 10000004 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 4456359 4456363 - 4390822 3 chr1 4456359 4456363 - 4456357 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 6 chr1 7501587 7501591 - 7436050 7 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 8 chr1 10000000 10000004 - 9934463 9 chr1 10000000 10000004 - 9999998 0 chr1 10000000 10000257 + 9934463 1 chr1 10000000 10000257 + 9999998 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390822 1 chr1 4456359 4456363 - 4456357 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 2 chr1 7501587 7501591 - 7436050 3 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 6 chr1 10000000 10000004 - 9934463 7 chr1 10000000 10000004 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390822 1 chr1 4456359 4456363 - 4456357 2 chr1 7501587 7501591 - 7436050 3 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 6 chr1 10000000 10000004 - 9934463 7 chr1 10000000 10000004 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390822 1 chr1 4456359 4456363 - 4456357 2 chr1 7501587 7501591 - 7436050 3 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 6 chr1 10000000 10000004 - 9934463 7 chr1 10000000 10000004 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjzm3hvf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzm3hvf7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 4456359 4456616 - 4456357 2 chr1 7501587 7501589 - 7436050 3 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 6 chr1 10000000 10000002 - 9934463 7 chr1 10000000 10000002 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 4456359 | 4456616 | a | 0 | ... | | chr1 | 4456359 | 4456616 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7501587 | 7501589 | a | 0 | ... | | chr1 | 7501587 | 7501589 | a | 0 | ... | | chr1 | 10000000 | 10000002 | a | 0 | ... | | chr1 | 10000000 | 10000002 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 4456359 4456616 - 4390822 3 chr1 4456359 4456616 - 4456357 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 6 chr1 7501587 7501589 - 7436050 7 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 8 chr1 10000000 10000002 - 9934463 9 chr1 10000000 10000002 - 9999998 0 chr1 10000000 10000257 + 9934463 1 chr1 10000000 10000257 + 9999998 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 4456359 4456616 - 4456357 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 2 chr1 7501587 7501589 - 7436050 3 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 6 chr1 10000000 10000002 - 9934463 7 chr1 10000000 10000002 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 4456359 4456616 - 4456357 2 chr1 7501587 7501589 - 7436050 3 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 6 chr1 10000000 10000002 - 9934463 7 chr1 10000000 10000002 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 4456359 4456616 - 4456357 2 chr1 7501587 7501589 - 7436050 3 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 6 chr1 10000000 10000002 - 9934463 7 chr1 10000000 10000002 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2tlmyeo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2tlmyeo0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 7501587 7501589 - 7436050 2 chr1 8017027 8019076 + 7951490 3 chr1 10000000 10000002 - 9934463 4 chr1 10000000 10000257 - 9934463 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8017027 | 8019076 | a | 0 | ... | | chr1 | 4456359 | 4456616 | a | 0 | ... | | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 7501587 | 7501589 | a | 0 | ... | | chr1 | 10000000 | 10000002 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4456359 4456616 - 4390822 3 chr1 7501587 7501589 - 7436050 0 chr1 8017027 8019076 + 7951490 4 chr1 10000000 10000002 - 9934463 2 chr1 10000000 10000257 - 9934463 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 7501587 7501589 - 7436050 2 chr1 8017027 8019076 + 7951490 3 chr1 10000000 10000002 - 9934463 4 chr1 10000000 10000257 - 9934463 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 7501587 7501589 - 7436050 2 chr1 8017027 8019076 + 7951490 3 chr1 10000000 10000002 - 9934463 4 chr1 10000000 10000257 - 9934463 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 7501587 7501589 - 7436050 2 chr1 8017027 8019076 + 7951490 3 chr1 10000000 10000002 - 9934463 4 chr1 10000000 10000257 - 9934463 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgqsyuxjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqsyuxjg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 919564 | 921707 | a | 0 | ... | | chr1 | 919564 | 921707 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 df2 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Expected Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9di_9tes/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9di_9tes/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 919564 | 921707 | a | 0 | ... | | chr1 | 919564 | 921707 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 df2 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Expected Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd3smunqk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3smunqk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 919564 | 921707 | a | 0 | ... | | chr1 | 919564 | 921707 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 df2 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Expected Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvgu35mrh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgu35mrh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2232268 | 2232269 | a | 0 | ... | | chr1 | 4720655 | 4720656 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 df2 Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 Actual Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 Expected Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpttmrajd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttmrajd2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2232268 | 2232269 | a | 0 | ... | | chr1 | 4720655 | 4720656 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 df2 Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 Actual Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 Expected Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp35rxp6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp35rxp6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 797760 | 804742 | a | 0 | ... | | chr1 | 5349582 | 5351801 | a | 0 | ... | | chr1 | 5971841 | 5981508 | a | 0 | ... | | chr1 | 341319 | 343309 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 341319 343309 + 2164325 0 chr1 797760 804742 + 1702892 1 chr1 5349582 5351801 + 2839053 2 chr1 5971841 5981508 + 3461312 df2 Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Actual Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Expected Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvqyj0x8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvqyj0x8n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 797760 | 804742 | a | 0 | ... | | chr1 | 5349582 | 5351801 | a | 0 | ... | | chr1 | 5971841 | 5981508 | a | 0 | ... | | chr1 | 341319 | 343309 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 341319 343309 + 2164325 0 chr1 797760 804742 + 1702892 1 chr1 5349582 5351801 + 2839053 2 chr1 5971841 5981508 + 3461312 df2 Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Actual Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Expected Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiadz29is/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiadz29is/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 5349582 5349839 - 5349325 3 chr1 5349582 5349839 - 5349581 0 chr1 5971841 5974958 - 5971584 1 chr1 5971841 5974958 - 5971840 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtkax5pv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtkax5pv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 5349582 5349839 - 5349325 3 chr1 5349582 5349839 - 5349581 0 chr1 5971841 5974958 - 5971584 1 chr1 5971841 5974958 - 5971840 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9u0rbkuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9u0rbkuh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 5349582 5349839 - 5347363 3 chr1 5349582 5349839 - 5349325 0 chr1 5971841 5974958 - 5969622 1 chr1 5971841 5974958 - 5971584 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgk2bffno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgk2bffno/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 5349582 5349839 - 5347363 3 chr1 5349582 5349839 - 5349325 0 chr1 5971841 5974958 - 5969622 1 chr1 5971841 5974958 - 5971584 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphos278jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphos278jk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5349582 | 5349583 | a | 0 | ... | | chr1 | 5971841 | 5971842 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ri2x81k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ri2x81k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6393486 + 2240332 11 chr1 6384213 6393486 + 2476749 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6904736 | 6905014 | a | 0 | ... | | chr1 | 6904736 | 6905014 | a | 0 | ... | | chr1 | 1875948 | 1880403 | a | 0 | ... | | chr1 | 1875948 | 1880403 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1857885 | 1864713 | a | 0 | ... | | chr1 | 1857885 | 1864713 | a | 0 | ... | | chr1 | 7477081 | 7480654 | a | 0 | ... | | chr1 | 7477081 | 7480654 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr1 1857885 1864713 - 2269306 15 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 12 chr1 2585164 2593524 - 1540495 13 chr1 2585164 2593524 - 6276711 10 chr1 3120336 3130271 + 1003748 11 chr1 3120336 3130271 + 5739964 6 chr1 3977291 3986661 + 147358 7 chr1 3977291 3986661 + 4883574 8 chr1 6384213 6393486 + 2240332 9 chr1 6384213 6393486 + 2476749 0 chr1 6904736 6905014 + 1965221 1 chr1 6904736 6905014 + 2760855 16 chr1 7477081 7480654 - 1389581 17 chr1 7477081 7480654 - 3333200 4 chr1 8282853 8289660 + 580575 5 chr1 8282853 8289660 + 4138972 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6393486 + 2240332 11 chr1 6384213 6393486 + 2476749 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6393486 + 2240332 11 chr1 6384213 6393486 + 2476749 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6393486 + 2240332 11 chr1 6384213 6393486 + 2476749 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmcsuguxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcsuguxx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6384214 + 2240332 11 chr1 6384213 6384214 + 2486021 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6904736 | 6905014 | a | 0 | ... | | chr1 | 6904736 | 6905014 | a | 0 | ... | | chr1 | 1875948 | 1880403 | a | 0 | ... | | chr1 | 1875948 | 1880403 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1857885 | 1864713 | a | 0 | ... | | chr1 | 1857885 | 1864713 | a | 0 | ... | | chr1 | 7477081 | 7480654 | a | 0 | ... | | chr1 | 7477081 | 7480654 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr1 1857885 1864713 - 2269306 15 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 12 chr1 2585164 2593524 - 1540495 13 chr1 2585164 2593524 - 6276711 10 chr1 3120336 3130271 + 1003748 11 chr1 3120336 3130271 + 5739964 6 chr1 3977291 3986661 + 147358 7 chr1 3977291 3986661 + 4883574 8 chr1 6384213 6384214 + 2240332 9 chr1 6384213 6384214 + 2486021 0 chr1 6904736 6905014 + 1965221 1 chr1 6904736 6905014 + 2760855 16 chr1 7477081 7480654 - 1389581 17 chr1 7477081 7480654 - 3333200 4 chr1 8282853 8289660 + 580575 5 chr1 8282853 8289660 + 4138972 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6384214 + 2240332 11 chr1 6384213 6384214 + 2486021 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6384214 + 2240332 11 chr1 6384213 6384214 + 2486021 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6384214 + 2240332 11 chr1 6384213 6384214 + 2486021 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6xjwicu5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xjwicu5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1792312 1 chr1 1875948 1876205 - 1810375 2 chr1 2585164 2585165 - 2519591 3 chr1 3120336 3120344 - 3054763 4 chr1 3977291 3977298 - 3911718 5 chr1 6384213 6384470 - 6318640 6 chr1 6904736 6904744 - 6839163 7 chr1 7477081 7477089 - 7411508 8 chr1 8282853 8283110 - 8217280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2585164 | 2585165 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 6904736 | 6904744 | a | 0 | ... | | chr1 | 1875948 | 1876205 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3977291 | 3977298 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | | chr1 | 3120336 | 3120344 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1857885 1857886 - 1792312 3 chr1 1875948 1876205 - 1810375 0 chr1 2585164 2585165 - 2519591 8 chr1 3120336 3120344 - 3054763 5 chr1 3977291 3977298 - 3911718 7 chr1 6384213 6384470 - 6318640 2 chr1 6904736 6904744 - 6839163 6 chr1 7477081 7477089 - 7411508 4 chr1 8282853 8283110 - 8217280 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1792312 1 chr1 1875948 1876205 - 1810375 2 chr1 2585164 2585165 - 2519591 3 chr1 3120336 3120344 - 3054763 4 chr1 3977291 3977298 - 3911718 5 chr1 6384213 6384470 - 6318640 6 chr1 6904736 6904744 - 6839163 7 chr1 7477081 7477089 - 7411508 8 chr1 8282853 8283110 - 8217280 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1792312 1 chr1 1875948 1876205 - 1810375 2 chr1 2585164 2585165 - 2519591 3 chr1 3120336 3120344 - 3054763 4 chr1 3977291 3977298 - 3911718 5 chr1 6384213 6384470 - 6318640 6 chr1 6904736 6904744 - 6839163 7 chr1 7477081 7477089 - 7411508 8 chr1 8282853 8283110 - 8217280 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1792312 1 chr1 1875948 1876205 - 1810375 2 chr1 2585164 2585165 - 2519591 3 chr1 3120336 3120344 - 3054763 4 chr1 3977291 3977298 - 3911718 5 chr1 6384213 6384470 - 6318640 6 chr1 6904736 6904744 - 6839163 7 chr1 7477081 7477089 - 7411508 8 chr1 8282853 8283110 - 8217280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptzrv4g70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzrv4g70/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 2585164 2585165 - 2585163 3 chr1 3120336 3120344 - 3120335 4 chr1 3977291 3977298 - 3977290 5 chr1 6384213 6384470 - 6384212 6 chr1 6904736 6904744 - 6904735 7 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282852 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2585164 | 2585165 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 6904736 | 6904744 | a | 0 | ... | | chr1 | 1875948 | 1876205 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3977291 | 3977298 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | | chr1 | 3120336 | 3120344 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1857885 1857886 - 1857884 3 chr1 1875948 1876205 - 1875947 0 chr1 2585164 2585165 - 2585163 8 chr1 3120336 3120344 - 3120335 5 chr1 3977291 3977298 - 3977290 7 chr1 6384213 6384470 - 6384212 2 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 4 chr1 8282853 8283110 - 8282852 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 2585164 2585165 - 2585163 3 chr1 3120336 3120344 - 3120335 4 chr1 3977291 3977298 - 3977290 5 chr1 6384213 6384470 - 6384212 6 chr1 6904736 6904744 - 6904735 7 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282852 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 2585164 2585165 - 2585163 3 chr1 3120336 3120344 - 3120335 4 chr1 3977291 3977298 - 3977290 5 chr1 6384213 6384470 - 6384212 6 chr1 6904736 6904744 - 6904735 7 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282852 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 2585164 2585165 - 2585163 3 chr1 3120336 3120344 - 3120335 4 chr1 3977291 3977298 - 3977290 5 chr1 6384213 6384470 - 6384212 6 chr1 6904736 6904744 - 6904735 7 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282852 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsf01u1bh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsf01u1bh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 3120336 3120337 - 3120335 3 chr1 3977291 3977298 - 3977290 4 chr1 6384213 6384470 - 6384212 5 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 7 chr1 8282853 8283110 - 8282852 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3120336 | 3120337 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 6904736 | 6904744 | a | 0 | ... | | chr1 | 1875948 | 1876205 | a | 0 | ... | | chr1 | 8282853 | 8283110 | a | 0 | ... | | chr1 | 3977291 | 3977298 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1857885 1857886 - 1857884 3 chr1 1875948 1876205 - 1875947 0 chr1 3120336 3120337 - 3120335 5 chr1 3977291 3977298 - 3977290 7 chr1 6384213 6384470 - 6384212 2 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 4 chr1 8282853 8283110 - 8282852 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 3120336 3120337 - 3120335 3 chr1 3977291 3977298 - 3977290 4 chr1 6384213 6384470 - 6384212 5 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 7 chr1 8282853 8283110 - 8282852 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 3120336 3120337 - 3120335 3 chr1 3977291 3977298 - 3977290 4 chr1 6384213 6384470 - 6384212 5 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 7 chr1 8282853 8283110 - 8282852 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 3120336 3120337 - 3120335 3 chr1 3977291 3977298 - 3977290 4 chr1 6384213 6384470 - 6384212 5 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 7 chr1 8282853 8283110 - 8282852 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84bzapq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84bzapq4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857628 1 chr1 1857885 1857886 - 1857884 2 chr1 1875948 1876205 - 1875691 3 chr1 1875948 1876205 - 1875947 4 chr1 3120336 3120337 - 3120079 5 chr1 3120336 3120337 - 3120335 6 chr1 3977291 3977298 - 3977034 7 chr1 3977291 3977298 - 3977290 8 chr1 6384213 6384470 - 6383956 9 chr1 6384213 6384470 - 6384212 10 chr1 6904736 6904744 - 6904479 11 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 14 chr1 8282853 8283110 - 8282596 15 chr1 8282853 8283110 - 8282852 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3120336 | 3120337 | a | 0 | ... | | chr1 | 3120336 | 3120337 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1857885 1857886 - 1857628 3 chr1 1857885 1857886 - 1857884 6 chr1 1875948 1876205 - 1875691 7 chr1 1875948 1876205 - 1875947 0 chr1 3120336 3120337 - 3120079 1 chr1 3120336 3120337 - 3120335 10 chr1 3977291 3977298 - 3977034 11 chr1 3977291 3977298 - 3977290 14 chr1 6384213 6384470 - 6383956 15 chr1 6384213 6384470 - 6384212 4 chr1 6904736 6904744 - 6904479 5 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282596 9 chr1 8282853 8283110 - 8282852 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857628 1 chr1 1857885 1857886 - 1857884 2 chr1 1875948 1876205 - 1875691 3 chr1 1875948 1876205 - 1875947 4 chr1 3120336 3120337 - 3120079 5 chr1 3120336 3120337 - 3120335 6 chr1 3977291 3977298 - 3977034 7 chr1 3977291 3977298 - 3977290 8 chr1 6384213 6384470 - 6383956 9 chr1 6384213 6384470 - 6384212 10 chr1 6904736 6904744 - 6904479 11 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 14 chr1 8282853 8283110 - 8282596 15 chr1 8282853 8283110 - 8282852 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857628 1 chr1 1857885 1857886 - 1857884 2 chr1 1875948 1876205 - 1875691 3 chr1 1875948 1876205 - 1875947 4 chr1 3120336 3120337 - 3120079 5 chr1 3120336 3120337 - 3120335 6 chr1 3977291 3977298 - 3977034 7 chr1 3977291 3977298 - 3977290 8 chr1 6384213 6384470 - 6383956 9 chr1 6384213 6384470 - 6384212 10 chr1 6904736 6904744 - 6904479 11 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 14 chr1 8282853 8283110 - 8282596 15 chr1 8282853 8283110 - 8282852 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857628 1 chr1 1857885 1857886 - 1857884 2 chr1 1875948 1876205 - 1875691 3 chr1 1875948 1876205 - 1875947 4 chr1 3120336 3120337 - 3120079 5 chr1 3120336 3120337 - 3120335 6 chr1 3977291 3977298 - 3977034 7 chr1 3977291 3977298 - 3977290 8 chr1 6384213 6384470 - 6383956 9 chr1 6384213 6384470 - 6384212 10 chr1 6904736 6904744 - 6904479 11 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 14 chr1 8282853 8283110 - 8282596 15 chr1 8282853 8283110 - 8282852 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp23pgj_h8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23pgj_h8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857880 1 chr1 1875948 1876205 - 1875943 2 chr1 3120336 3120337 - 3120331 3 chr1 3977291 3977298 - 3977286 4 chr1 6384213 6384470 - 6384208 5 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 7 chr1 8282853 8283110 - 8282848 9 chr17 9999999 10000015 + 9999742 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3120336 | 3120337 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 6904736 | 6904744 | a | 0 | ... | | chr1 | 1875948 | 1876205 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8282853 | 8283110 | a | 0 | ... | | chr1 | 3977291 | 3977298 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1857885 1857886 - 1857880 3 chr1 1875948 1876205 - 1875943 0 chr1 3120336 3120337 - 3120331 5 chr1 3977291 3977298 - 3977286 7 chr1 6384213 6384470 - 6384208 2 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 4 chr1 8282853 8283110 - 8282848 8 chr17 9999999 10000015 + 9999742 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857880 1 chr1 1875948 1876205 - 1875943 2 chr1 3120336 3120337 - 3120331 3 chr1 3977291 3977298 - 3977286 4 chr1 6384213 6384470 - 6384208 5 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 7 chr1 8282853 8283110 - 8282848 9 chr17 9999999 10000015 + 9999742 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857880 1 chr1 1875948 1876205 - 1875943 2 chr1 3120336 3120337 - 3120331 3 chr1 3977291 3977298 - 3977286 4 chr1 6384213 6384470 - 6384208 5 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 7 chr1 8282853 8283110 - 8282848 8 chr17 9999999 10000015 + 9999742 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857880 1 chr1 1875948 1876205 - 1875943 2 chr1 3120336 3120337 - 3120331 3 chr1 3977291 3977298 - 3977286 4 chr1 6384213 6384470 - 6384208 5 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 7 chr1 8282853 8283110 - 8282848 8 chr17 9999999 10000015 + 9999742 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3nzs8dz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3nzs8dz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyehosf1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyehosf1f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwy342k63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwy342k63/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpry8w5jfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpry8w5jfc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9rtzccql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9rtzccql/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkkg_f163/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkg_f163/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppsiup88n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppsiup88n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr2 5 10 - 65528 4 chr2 65537 65545 + 65528 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 65537 | 65545 | a | 0 | ... | | chr2 | 5 | 10 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr2 5 10 - 65528 0 chr2 65537 65545 + 65528 df2 Chromosome Start End Strand Distance 3 chr2 5 10 - 65528 4 chr2 65537 65545 + 65528 Actual Chromosome Start End Strand Distance 0 chr2 5 10 - 65528 1 chr2 65537 65545 + 65528 Expected Chromosome Start End Strand Distance 0 chr2 5 10 - 65528 1 chr2 65537 65545 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyd3kyfc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyd3kyfc_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 777296 | 778138 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 df2 Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 Actual Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 Expected Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3tug85_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3tug85_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj5p10xmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5p10xmb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2gz49d5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gz49d5n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ynbbluu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ynbbluu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmcmjevts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcmjevts/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvq0mquh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvq0mquh3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 df2 Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 Actual Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 Expected Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfql8qyi5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfql8qyi5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 1 chr1 2104303 2108644 - 2863760 2 chr1 2846879 2848496 - 2123908 3 chr1 4381746 4386060 - 586344 4 chr1 4492514 4499564 + 472840 5 chr1 8228265 8236308 - 3255861 6 chr1 9502681 9506995 + 4530277 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7598 | a | 0 | ... | | chr1 | 4492514 | 4499564 | a | 0 | ... | | chr1 | 9502681 | 9506995 | a | 0 | ... | | chr1 | 8228265 | 8236308 | a | 0 | ... | | chr1 | 2846879 | 2848496 | a | 0 | ... | | chr1 | 4381746 | 4386060 | a | 0 | ... | | chr1 | 2104303 | 2108644 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 6 chr1 2104303 2108644 - 2863760 4 chr1 2846879 2848496 - 2123908 5 chr1 4381746 4386060 - 586344 1 chr1 4492514 4499564 + 472840 3 chr1 8228265 8236308 - 3255861 2 chr1 9502681 9506995 + 4530277 df2 Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 1 chr1 2104303 2108644 - 2863760 2 chr1 2846879 2848496 - 2123908 3 chr1 4381746 4386060 - 586344 4 chr1 4492514 4499564 + 472840 5 chr1 8228265 8236308 - 3255861 6 chr1 9502681 9506995 + 4530277 Actual Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 1 chr1 2104303 2108644 - 2863760 2 chr1 2846879 2848496 - 2123908 3 chr1 4381746 4386060 - 586344 4 chr1 4492514 4499564 + 472840 5 chr1 8228265 8236308 - 3255861 6 chr1 9502681 9506995 + 4530277 Expected Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 1 chr1 2104303 2108644 - 2863760 2 chr1 2846879 2848496 - 2123908 3 chr1 4381746 4386060 - 586344 4 chr1 4492514 4499564 + 472840 5 chr1 8228265 8236308 - 3255861 6 chr1 9502681 9506995 + 4530277 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyh56lv8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyh56lv8h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 2 chr1 1 3 - 1 3 chr1 1 3 - 938 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 57492 9 chr1 65537 65539 + 64595 10 chr1 65537 65539 + 57492 11 chr1 65537 65539 + 64595 12 chr1 65537 65539 - 57492 13 chr1 65537 65539 - 64595 14 chr1 65537 65539 - 57492 15 chr1 65537 65539 - 64595 16 chr1 65537 65539 - 57492 17 chr1 65537 65539 - 64595 18 chr1 65537 65539 - 57492 19 chr1 65537 65539 - 64595 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 3 - 1 7 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 10 chr1 2 4 - 937 11 chr1 2 4 - 8040 16 chr1 4 6 - 935 17 chr1 4 6 - 8038 0 chr1 65537 65539 + 57492 4 chr1 65537 65539 + 57492 8 chr1 65537 65539 - 57492 12 chr1 65537 65539 - 57492 14 chr1 65537 65539 - 57492 18 chr1 65537 65539 - 57492 1 chr1 65537 65539 + 64595 5 chr1 65537 65539 + 64595 9 chr1 65537 65539 - 64595 13 chr1 65537 65539 - 64595 15 chr1 65537 65539 - 64595 19 chr1 65537 65539 - 64595 df2 Chromosome Start End Strand Distance 2 chr1 1 3 - 1 3 chr1 1 3 - 938 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 57492 10 chr1 65537 65539 + 57492 12 chr1 65537 65539 - 57492 14 chr1 65537 65539 - 57492 16 chr1 65537 65539 - 57492 18 chr1 65537 65539 - 57492 9 chr1 65537 65539 + 64595 11 chr1 65537 65539 + 64595 13 chr1 65537 65539 - 64595 15 chr1 65537 65539 - 64595 17 chr1 65537 65539 - 64595 19 chr1 65537 65539 - 64595 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 57492 9 chr1 65537 65539 + 57492 10 chr1 65537 65539 + 64595 11 chr1 65537 65539 + 64595 12 chr1 65537 65539 - 57492 13 chr1 65537 65539 - 57492 14 chr1 65537 65539 - 57492 15 chr1 65537 65539 - 57492 16 chr1 65537 65539 - 64595 17 chr1 65537 65539 - 64595 18 chr1 65537 65539 - 64595 19 chr1 65537 65539 - 64595 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 57492 9 chr1 65537 65539 + 57492 10 chr1 65537 65539 + 64595 11 chr1 65537 65539 + 64595 12 chr1 65537 65539 - 57492 13 chr1 65537 65539 - 57492 14 chr1 65537 65539 - 57492 15 chr1 65537 65539 - 57492 16 chr1 65537 65539 - 64595 17 chr1 65537 65539 - 64595 18 chr1 65537 65539 - 64595 19 chr1 65537 65539 - 64595 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4l4hs22d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4l4hs22d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 2 chr1 1 3 - 1 3 chr1 1 3 - 938 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 49452 9 chr1 65537 65539 + 63658 10 chr1 65537 65539 + 49452 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 49452 13 chr1 65537 65539 - 63658 14 chr1 65537 65539 - 49452 15 chr1 65537 65539 - 63658 16 chr1 65537 65539 - 49452 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 49452 19 chr1 65537 65539 - 63658 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 3 - 1 7 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 10 chr1 2 4 - 937 11 chr1 2 4 - 8040 16 chr1 4 6 - 935 17 chr1 4 6 - 8038 0 chr1 65537 65539 + 49452 4 chr1 65537 65539 + 49452 8 chr1 65537 65539 - 49452 12 chr1 65537 65539 - 49452 14 chr1 65537 65539 - 49452 18 chr1 65537 65539 - 49452 1 chr1 65537 65539 + 63658 5 chr1 65537 65539 + 63658 9 chr1 65537 65539 - 63658 13 chr1 65537 65539 - 63658 15 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 df2 Chromosome Start End Strand Distance 2 chr1 1 3 - 1 3 chr1 1 3 - 938 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 49452 10 chr1 65537 65539 + 49452 12 chr1 65537 65539 - 49452 14 chr1 65537 65539 - 49452 16 chr1 65537 65539 - 49452 18 chr1 65537 65539 - 49452 9 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 13 chr1 65537 65539 - 63658 15 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 49452 9 chr1 65537 65539 + 49452 10 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 49452 13 chr1 65537 65539 - 49452 14 chr1 65537 65539 - 49452 15 chr1 65537 65539 - 49452 16 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 49452 9 chr1 65537 65539 + 49452 10 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 49452 13 chr1 65537 65539 - 49452 14 chr1 65537 65539 - 49452 15 chr1 65537 65539 - 49452 16 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy3vp07lp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3vp07lp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 2 chr1 1 3 - 1 3 chr1 1 3 - 938 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 57494 9 chr1 65537 65539 + 63658 10 chr1 65537 65539 + 57494 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 57494 13 chr1 65537 65539 - 63658 14 chr1 65537 65539 - 57494 15 chr1 65537 65539 - 63658 16 chr1 65537 65539 - 57494 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 57494 19 chr1 65537 65539 - 63658 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 3 - 1 7 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 10 chr1 2 4 - 1 11 chr1 2 4 - 937 16 chr1 4 6 - 3 17 chr1 4 6 - 935 0 chr1 65537 65539 + 57494 4 chr1 65537 65539 + 57494 8 chr1 65537 65539 - 57494 12 chr1 65537 65539 - 57494 14 chr1 65537 65539 - 57494 18 chr1 65537 65539 - 57494 1 chr1 65537 65539 + 63658 5 chr1 65537 65539 + 63658 9 chr1 65537 65539 - 63658 13 chr1 65537 65539 - 63658 15 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 df2 Chromosome Start End Strand Distance 2 chr1 1 3 - 1 3 chr1 1 3 - 938 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 57494 10 chr1 65537 65539 + 57494 12 chr1 65537 65539 - 57494 14 chr1 65537 65539 - 57494 16 chr1 65537 65539 - 57494 18 chr1 65537 65539 - 57494 9 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 13 chr1 65537 65539 - 63658 15 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 57494 9 chr1 65537 65539 + 57494 10 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 57494 13 chr1 65537 65539 - 57494 14 chr1 65537 65539 - 57494 15 chr1 65537 65539 - 57494 16 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 57494 9 chr1 65537 65539 + 57494 10 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 57494 13 chr1 65537 65539 - 57494 14 chr1 65537 65539 - 57494 15 chr1 65537 65539 - 57494 16 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg4v67ls4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4v67ls4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 683 1 chr1 1 258 + 6793 2 chr1 1 3 - 1 3 chr1 1 3 - 938 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 48370 9 chr1 65537 65539 + 51438 10 chr1 65537 65539 + 48370 11 chr1 65537 65539 + 51438 12 chr1 65537 65539 - 48370 13 chr1 65537 65539 - 51438 14 chr1 65537 65539 - 48370 15 chr1 65537 65539 - 51438 16 chr1 65537 65539 - 48370 17 chr1 65537 65539 - 51438 18 chr1 65537 65539 - 48370 19 chr1 65537 65539 - 51438 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 3 - 1 7 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 6793 10 chr1 2 4 - 1 11 chr1 2 4 - 937 16 chr1 4 6 - 3 17 chr1 4 6 - 935 0 chr1 65537 65539 + 48370 4 chr1 65537 65539 + 48370 8 chr1 65537 65539 - 48370 12 chr1 65537 65539 - 48370 14 chr1 65537 65539 - 48370 18 chr1 65537 65539 - 48370 1 chr1 65537 65539 + 51438 5 chr1 65537 65539 + 51438 9 chr1 65537 65539 - 51438 13 chr1 65537 65539 - 51438 15 chr1 65537 65539 - 51438 19 chr1 65537 65539 - 51438 df2 Chromosome Start End Strand Distance 2 chr1 1 3 - 1 3 chr1 1 3 - 938 0 chr1 1 258 + 683 1 chr1 1 258 + 6793 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 48370 10 chr1 65537 65539 + 48370 12 chr1 65537 65539 - 48370 14 chr1 65537 65539 - 48370 16 chr1 65537 65539 - 48370 18 chr1 65537 65539 - 48370 9 chr1 65537 65539 + 51438 11 chr1 65537 65539 + 51438 13 chr1 65537 65539 - 51438 15 chr1 65537 65539 - 51438 17 chr1 65537 65539 - 51438 19 chr1 65537 65539 - 51438 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 6793 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 48370 9 chr1 65537 65539 + 48370 10 chr1 65537 65539 + 51438 11 chr1 65537 65539 + 51438 12 chr1 65537 65539 - 48370 13 chr1 65537 65539 - 48370 14 chr1 65537 65539 - 48370 15 chr1 65537 65539 - 48370 16 chr1 65537 65539 - 51438 17 chr1 65537 65539 - 51438 18 chr1 65537 65539 - 51438 19 chr1 65537 65539 - 51438 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 6793 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 48370 9 chr1 65537 65539 + 48370 10 chr1 65537 65539 + 51438 11 chr1 65537 65539 + 51438 12 chr1 65537 65539 - 48370 13 chr1 65537 65539 - 48370 14 chr1 65537 65539 - 48370 15 chr1 65537 65539 - 48370 16 chr1 65537 65539 - 51438 17 chr1 65537 65539 - 51438 18 chr1 65537 65539 - 51438 19 chr1 65537 65539 - 51438 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpecl1m2m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpecl1m2m4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 939 2 chr1 1 2 - 2 3 chr1 1 2 - 939 4 chr1 1 2 - 2 5 chr1 1 2 - 939 6 chr1 1 2 - 2 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9502681 | 9502684 | a | 0 | ... | | chr1 | 9502681 | 9502684 | a | 0 | ... | | chr1 | 8584 | 17168 | a | 0 | ... | | chr1 | 8584 | 17168 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 12 chr1 1 2 - 2 14 chr1 1 2 - 2 16 chr1 1 2 - 2 18 chr1 1 2 - 2 13 chr1 1 2 - 939 15 chr1 1 2 - 939 17 chr1 1 2 - 939 19 chr1 1 2 - 939 10 chr1 3 6 - 2 11 chr1 3 6 - 935 4 chr1 940 1880 - 935 5 chr1 940 1880 - 939 8 chr1 7050 14100 - 5171 9 chr1 7050 14100 - 7045 6 chr1 8043 8044 - 541 7 chr1 8043 8044 - 6164 2 chr1 8584 17168 - 541 3 chr1 8584 17168 - 6705 0 chr1 9502681 9502684 - 9485514 1 chr1 9502681 9502684 - 9488582 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 2 chr1 1 2 - 2 4 chr1 1 2 - 2 6 chr1 1 2 - 2 1 chr1 1 2 - 939 3 chr1 1 2 - 939 5 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 939 5 chr1 1 2 - 939 6 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 939 5 chr1 1 2 - 939 6 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgw6u7yog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgw6u7yog/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 939 2 chr1 1 2 - 2 3 chr1 1 2 - 939 4 chr1 1 2 - 2 5 chr1 1 2 - 939 6 chr1 1 2 - 2 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9502681 | 9502684 | a | 0 | ... | | chr1 | 9502681 | 9502684 | a | 0 | ... | | chr1 | 8584 | 17168 | a | 0 | ... | | chr1 | 8584 | 17168 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 12 chr1 1 2 - 2 14 chr1 1 2 - 2 16 chr1 1 2 - 2 18 chr1 1 2 - 2 13 chr1 1 2 - 939 15 chr1 1 2 - 939 17 chr1 1 2 - 939 19 chr1 1 2 - 939 10 chr1 3 6 - 2 11 chr1 3 6 - 935 4 chr1 940 1880 - 935 5 chr1 940 1880 - 939 8 chr1 7050 14100 - 5171 9 chr1 7050 14100 - 7045 6 chr1 8043 8044 - 541 7 chr1 8043 8044 - 6164 2 chr1 8584 17168 - 541 3 chr1 8584 17168 - 6705 0 chr1 9502681 9502684 - 9485514 1 chr1 9502681 9502684 - 9488582 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 2 chr1 1 2 - 2 4 chr1 1 2 - 2 6 chr1 1 2 - 2 1 chr1 1 2 - 939 3 chr1 1 2 - 939 5 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 939 5 chr1 1 2 - 939 6 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 939 5 chr1 1 2 - 939 6 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7rnfspqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7rnfspqa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpobiuvoab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobiuvoab/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa2rn94b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2rn94b3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_lgcsesu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_lgcsesu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt7glub96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7glub96/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_z4o0928/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_z4o0928/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2137398 - 1758191 1 chr1 2130767 2137398 - 3215459 2 chr1 5054106 5057810 + 295047 3 chr1 5054106 5057810 + 1150943 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5054106 | 5057810 | a | 0 | ... | | chr1 | 5054106 | 5057810 | a | 0 | ... | | chr1 | 2130767 | 2137398 | a | 0 | ... | | chr1 | 2130767 | 2137398 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2130767 2137398 - 1758191 3 chr1 2130767 2137398 - 3215459 0 chr1 5054106 5057810 + 295047 1 chr1 5054106 5057810 + 1150943 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2137398 - 1758191 1 chr1 2130767 2137398 - 3215459 2 chr1 5054106 5057810 + 295047 3 chr1 5054106 5057810 + 1150943 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2137398 - 1758191 1 chr1 2130767 2137398 - 3215459 2 chr1 5054106 5057810 + 295047 3 chr1 5054106 5057810 + 1150943 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2137398 - 1758191 1 chr1 2130767 2137398 - 3215459 2 chr1 5054106 5057810 + 295047 3 chr1 5054106 5057810 + 1150943 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9zisne_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zisne_d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpli72lv_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpli72lv_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph5t67q4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5t67q4c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe6e4grrt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6e4grrt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9voarufd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9voarufd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 1 chr1 2130767 2130768 + 2130766 2 chr1 2130767 2130768 - 2130765 3 chr1 2130767 2130768 - 2130766 4 chr1 2130767 2130768 - 2130765 5 chr1 2130767 2130768 - 2130766 6 chr1 2130767 2130768 - 2130765 7 chr1 2130767 2130768 - 2130766 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 2 chr1 2130767 2130768 - 2130765 4 chr1 2130767 2130768 - 2130765 6 chr1 2130767 2130768 - 2130765 1 chr1 2130767 2130768 + 2130766 3 chr1 2130767 2130768 - 2130766 5 chr1 2130767 2130768 - 2130766 7 chr1 2130767 2130768 - 2130766 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 2 chr1 2130767 2130768 - 2130765 4 chr1 2130767 2130768 - 2130765 6 chr1 2130767 2130768 - 2130765 1 chr1 2130767 2130768 + 2130766 3 chr1 2130767 2130768 - 2130766 5 chr1 2130767 2130768 - 2130766 7 chr1 2130767 2130768 - 2130766 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 1 chr1 2130767 2130768 + 2130766 2 chr1 2130767 2130768 - 2130765 3 chr1 2130767 2130768 - 2130765 4 chr1 2130767 2130768 - 2130765 5 chr1 2130767 2130768 - 2130766 6 chr1 2130767 2130768 - 2130766 7 chr1 2130767 2130768 - 2130766 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 1 chr1 2130767 2130768 + 2130766 2 chr1 2130767 2130768 - 2130765 3 chr1 2130767 2130768 - 2130765 4 chr1 2130767 2130768 - 2130765 5 chr1 2130767 2130768 - 2130766 6 chr1 2130767 2130768 - 2130766 7 chr1 2130767 2130768 - 2130766 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpay0xt8gp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpay0xt8gp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 14 chrX 5845437 5845723 - 449422 15 chrX 7883280 7888139 - 2487265 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 9587 + 660069 5 chr1 2 9587 + 1209178 6 chr1 5416362 5422259 - 1826971 7 chr1 5416362 5422259 - 3815027 10 chrX 5845437 5845723 - 449422 2 chr1 7107361 7116114 + 133116 3 chr1 7107361 7116114 + 2121172 11 chrX 7883280 7888139 - 2487265 0 chr1 8425326 8429580 + 807706 1 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 df2 Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 14 chrX 5845437 5845723 - 449422 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 15 chrX 7883280 7888139 - 2487265 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 Actual Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 10 chrX 5845437 5845723 - 449422 11 chrX 7883280 7888139 - 2487265 Expected Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 10 chrX 5845437 5845723 - 449422 11 chrX 7883280 7888139 - 2487265 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzdpuopha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzdpuopha/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 14 chrX 5845437 5845723 - 449422 15 chrX 7883280 7888139 - 2487265 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 9587 + 660069 5 chr1 2 9587 + 1209178 6 chr1 5416362 5422259 - 1826971 7 chr1 5416362 5422259 - 3815027 10 chrX 5845437 5845723 - 449422 2 chr1 7107361 7116114 + 133116 3 chr1 7107361 7116114 + 2121172 11 chrX 7883280 7888139 - 2487265 0 chr1 8425326 8429580 + 807706 1 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 df2 Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 14 chrX 5845437 5845723 - 449422 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 15 chrX 7883280 7888139 - 2487265 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 Actual Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 10 chrX 5845437 5845723 - 449422 11 chrX 7883280 7888139 - 2487265 Expected Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 10 chrX 5845437 5845723 - 449422 11 chrX 7883280 7888139 - 2487265 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3hk7tvit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3hk7tvit/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 4197598 3 chr1 5416362 5422259 - 4577742 4 chr1 7107361 7116114 + 2883887 5 chr1 7107361 7116114 + 5888597 6 chr1 8425326 8429580 + 1570421 7 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 14 chrX 5845437 5845723 - 448148 15 chrX 7883280 7888139 - 2485991 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 9587 + 660069 5 chr1 2 9587 + 1209178 6 chr1 5416362 5422259 - 4197598 7 chr1 5416362 5422259 - 4577742 10 chrX 5845437 5845723 - 448148 2 chr1 7107361 7116114 + 2883887 3 chr1 7107361 7116114 + 5888597 11 chrX 7883280 7888139 - 2485991 0 chr1 8425326 8429580 + 1570421 1 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 df2 Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 4197598 3 chr1 5416362 5422259 - 4577742 14 chrX 5845437 5845723 - 448148 4 chr1 7107361 7116114 + 2883887 5 chr1 7107361 7116114 + 5888597 15 chrX 7883280 7888139 - 2485991 6 chr1 8425326 8429580 + 1570421 7 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 Actual Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 4197598 3 chr1 5416362 5422259 - 4577742 4 chr1 7107361 7116114 + 2883887 5 chr1 7107361 7116114 + 5888597 6 chr1 8425326 8429580 + 1570421 7 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 10 chrX 5845437 5845723 - 448148 11 chrX 7883280 7888139 - 2485991 Expected Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 4197598 3 chr1 5416362 5422259 - 4577742 4 chr1 7107361 7116114 + 2883887 5 chr1 7107361 7116114 + 5888597 6 chr1 8425326 8429580 + 1570421 7 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 10 chrX 5845437 5845723 - 448148 11 chrX 7883280 7888139 - 2485991 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsn55dokh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsn55dokh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjpaujdij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpaujdij/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr2 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmk7yzyv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk7yzyv8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr2 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyb1445s0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyb1445s0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr2 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzm2o22th/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzm2o22th/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplu45ue01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplu45ue01/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpypn6_nmu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpypn6_nmu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwykrezjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwykrezjf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr19 | 2455990 | 2458227 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 df2 Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 Actual Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 Expected Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxeqvv6to/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxeqvv6to/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7548952 | 7549025 | a | 0 | ... | | chr1 | 7548952 | 7549025 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 df2 Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Actual Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Expected Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpltnbh9u0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpltnbh9u0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7548952 | 7549025 | a | 0 | ... | | chr1 | 7548952 | 7549025 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 df2 Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Actual Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Expected Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpktx9x0iz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktx9x0iz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 7548952 | 7549025 | a | 0 | ... | | chr1 | 7548952 | 7549025 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 df2 Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00plyybe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00plyybe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmm4aumit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmm4aumit/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz5h5btoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5h5btoh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf48q4iru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf48q4iru/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 + 93 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 + 93 df2 Chromosome Start End Strand Distance 0 chr2 1 2 + 93 Actual Chromosome Start End Strand Distance 0 chr2 1 2 + 93 Expected Chromosome Start End Strand Distance 0 chr2 1 2 + 93 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp375pgjgq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp375pgjgq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxo23cb4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxo23cb4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsvorbd67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvorbd67/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 df2 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 Actual Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 Expected Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_lc4qcs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_lc4qcs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 df2 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 Actual Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 Expected Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppobfqim6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppobfqim6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 df2 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 Actual Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 Expected Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv778fq_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv778fq_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb324fvve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb324fvve/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 25 + 22 1 chr1 2 25 + 65513 2 chr1 2 259 - 65279 3 chr1 2 3 - 21 4 chr1 2 3 - 44 5 chr1 2 5 - 19 6 chr1 2 5 - 42 7 chr1 2 5 - 19 8 chr1 2 5 - 42 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 25 | a | 0 | ... | | chr1 | 2 | 25 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 5 | a | 0 | ... | | chr1 | 2 | 5 | a | 0 | ... | | chr1 | 2 | 5 | a | 0 | ... | | chr1 | 2 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2 3 - 21 3 chr1 2 3 - 44 5 chr1 2 5 - 19 7 chr1 2 5 - 19 6 chr1 2 5 - 42 8 chr1 2 5 - 42 0 chr1 2 25 + 22 1 chr1 2 25 + 65513 4 chr1 2 259 - 65279 df2 Chromosome Start End Strand Distance 3 chr1 2 3 - 21 4 chr1 2 3 - 44 5 chr1 2 5 - 19 7 chr1 2 5 - 19 6 chr1 2 5 - 42 8 chr1 2 5 - 42 0 chr1 2 25 + 22 1 chr1 2 25 + 65513 2 chr1 2 259 - 65279 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 21 1 chr1 2 3 - 44 2 chr1 2 5 - 19 3 chr1 2 5 - 19 4 chr1 2 5 - 42 5 chr1 2 5 - 42 6 chr1 2 25 + 22 7 chr1 2 25 + 65513 8 chr1 2 259 - 65279 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 21 1 chr1 2 3 - 44 2 chr1 2 5 - 19 3 chr1 2 5 - 19 4 chr1 2 5 - 42 5 chr1 2 5 - 42 6 chr1 2 25 + 22 7 chr1 2 25 + 65513 8 chr1 2 259 - 65279 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp12_tjy1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12_tjy1j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 43 4 chr1 1 4 - 20 5 chr1 1 4 - 43 6 chr1 1 4 - 20 7 chr1 1 4 - 43 8 chr1 65537 65540 - 65235 9 chr1 65537 65540 - 65258 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 + 20 4 chr1 1 4 - 20 6 chr1 1 4 - 20 8 chr1 1 4 - 20 1 chr1 1 4 + 43 5 chr1 1 4 - 43 7 chr1 1 4 - 43 9 chr1 1 4 - 43 2 chr1 65537 65540 - 65235 3 chr1 65537 65540 - 65258 df2 Chromosome Start End Strand Distance 0 chr1 1 4 + 20 2 chr1 1 4 - 20 4 chr1 1 4 - 20 6 chr1 1 4 - 20 1 chr1 1 4 + 43 3 chr1 1 4 - 43 5 chr1 1 4 - 43 7 chr1 1 4 - 43 8 chr1 65537 65540 - 65235 9 chr1 65537 65540 - 65258 Actual Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 20 4 chr1 1 4 - 20 5 chr1 1 4 - 43 6 chr1 1 4 - 43 7 chr1 1 4 - 43 8 chr1 65537 65540 - 65235 9 chr1 65537 65540 - 65258 Expected Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 20 4 chr1 1 4 - 20 5 chr1 1 4 - 43 6 chr1 1 4 - 43 7 chr1 1 4 - 43 8 chr1 65537 65540 - 65235 9 chr1 65537 65540 - 65258 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpce6q6kr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpce6q6kr5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 43 4 chr1 1 4 - 20 5 chr1 1 4 - 43 6 chr1 65537 65540 - 65235 7 chr1 65537 65540 - 65258 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 + 20 4 chr1 1 4 - 20 6 chr1 1 4 - 20 1 chr1 1 4 + 43 5 chr1 1 4 - 43 7 chr1 1 4 - 43 2 chr1 65537 65540 - 65235 3 chr1 65537 65540 - 65258 df2 Chromosome Start End Strand Distance 0 chr1 1 4 + 20 2 chr1 1 4 - 20 4 chr1 1 4 - 20 1 chr1 1 4 + 43 3 chr1 1 4 - 43 5 chr1 1 4 - 43 6 chr1 65537 65540 - 65235 7 chr1 65537 65540 - 65258 Actual Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 20 4 chr1 1 4 - 43 5 chr1 1 4 - 43 6 chr1 65537 65540 - 65235 7 chr1 65537 65540 - 65258 Expected Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 20 4 chr1 1 4 - 43 5 chr1 1 4 - 43 6 chr1 65537 65540 - 65235 7 chr1 65537 65540 - 65258 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9nm24h4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9nm24h4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6272248 6273856 + 1900002 1 chr1 6272248 6273856 + 5962055 2 chr1 8959181 8968729 + 4586935 3 chr1 8959181 8968729 + 8648988 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8959181 | 8968729 | a | 0 | ... | | chr1 | 8959181 | 8968729 | a | 0 | ... | | chr1 | 6272248 | 6273856 | a | 0 | ... | | chr1 | 6272248 | 6273856 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 6272248 6273856 + 1900002 3 chr1 6272248 6273856 + 5962055 0 chr1 8959181 8968729 + 4586935 1 chr1 8959181 8968729 + 8648988 df2 Chromosome Start End Strand Distance 0 chr1 6272248 6273856 + 1900002 1 chr1 6272248 6273856 + 5962055 2 chr1 8959181 8968729 + 4586935 3 chr1 8959181 8968729 + 8648988 Actual Chromosome Start End Strand Distance 0 chr1 6272248 6273856 + 1900002 1 chr1 6272248 6273856 + 5962055 2 chr1 8959181 8968729 + 4586935 3 chr1 8959181 8968729 + 8648988 Expected Chromosome Start End Strand Distance 0 chr1 6272248 6273856 + 1900002 1 chr1 6272248 6273856 + 5962055 2 chr1 8959181 8968729 + 4586935 3 chr1 8959181 8968729 + 8648988 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfhqgbt7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfhqgbt7o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8i_qlnt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8i_qlnt7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp26a9vhm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp26a9vhm5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9v15oe9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9v15oe9w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0p8y9gqw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0p8y9gqw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjkd640u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjkd640u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp03am2lqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03am2lqm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4642731 | 4648603 | a | 0 | ... | | chr1 | 4642731 | 4648603 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 df2 Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 Actual Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 Expected Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnliyq8o8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnliyq8o8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw2bn1gw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw2bn1gw3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqvl1z0i5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvl1z0i5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1zgwlx31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zgwlx31/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 df2 Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 Actual Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 Expected Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7322hhha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7322hhha/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv0st42zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv0st42zh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5362ci3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5362ci3q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5jwkvyxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jwkvyxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqx9gks2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqx9gks2q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp54f1ks3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54f1ks3l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp03hxiw0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03hxiw0j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4459970 | a | 0 | ... | | chr1 | 4459968 | 4459970 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpji1he918/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpji1he918/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4459970 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbck7zsql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbck7zsql/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 4614322 4621281 + 154353 2 chr8 8355653 8355655 + 3734373 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr8 | 8355653 | 8355655 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4614322 4621281 + 154353 1 chr8 8355653 8355655 + 3734373 df2 Chromosome Start End Strand Distance 1 chr1 4614322 4621281 + 154353 2 chr8 8355653 8355655 + 3734373 Actual Chromosome Start End Strand Distance 0 chr1 4614322 4621281 + 154353 1 chr8 8355653 8355655 + 3734373 Expected Chromosome Start End Strand Distance 0 chr1 4614322 4621281 + 154353 1 chr8 8355653 8355655 + 3734373 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjvqmhrvt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvqmhrvt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4238 | a | 0 | ... | | chr1 | 519643 | 529390 | a | 0 | ... | | chr1 | 9778855 | 9788814 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 df2 Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 Actual Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 Expected Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuovzavji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuovzavji/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4238 | a | 0 | ... | | chr1 | 1 | 4238 | a | 0 | ... | | chr1 | 519643 | 529390 | a | 0 | ... | | chr1 | 519643 | 529390 | a | 0 | ... | | chr1 | 9778855 | 9788814 | a | 0 | ... | | chr1 | 9778855 | 9788814 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 df2 Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 Actual Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 Expected Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2s183eoo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2s183eoo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 7 chr2 8 265 - 5624841 8 chr2 8 265 - 5624841 9 chr2 8 265 - 5624841 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8 | 265 | a | 0 | ... | | chr1 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 2 chr2 8 265 - 5624841 3 chr2 8 265 - 5624841 4 chr2 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 df2 Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 7 chr2 8 265 - 5624841 8 chr2 8 265 - 5624841 9 chr2 8 265 - 5624841 Actual Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 2 chr2 8 265 - 5624841 3 chr2 8 265 - 5624841 4 chr2 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 Expected Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 2 chr2 8 265 - 5624841 3 chr2 8 265 - 5624841 4 chr2 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb1ji0sbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1ji0sbx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 4 chr7 519643 529390 - 5095716 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 293 | a | 0 | ... | | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5629342 | a | 0 | ... | | chr7 | 519643 | 529390 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 5 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 4 chr7 5625105 5629342 - 5095716 2 chr7 5625105 5635064 + 5095716 3 chr7 5625105 5635064 + 5095716 df2 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 4 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 Actual Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Expected Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4y3ilshz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4y3ilshz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 4 chr7 519643 529390 - 5095716 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 293 | a | 0 | ... | | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5629342 | a | 0 | ... | | chr7 | 519643 | 529390 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 5 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 4 chr7 5625105 5629342 - 5095716 2 chr7 5625105 5635064 + 5095716 3 chr7 5625105 5635064 + 5095716 df2 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 4 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 Actual Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Expected Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk930trl0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk930trl0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 4 chr7 519643 529390 - 5095716 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 293 | a | 0 | ... | | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5629342 | a | 0 | ... | | chr7 | 519643 | 529390 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 5 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 4 chr7 5625105 5629342 - 5095716 2 chr7 5625105 5635064 + 5095716 3 chr7 5625105 5635064 + 5095716 df2 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 4 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 Actual Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Expected Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2w0cz04u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2w0cz04u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 5625105 5625302 - 5619510 2 chr1 5625105 5625302 - 5623070 3 chr2 5625105 5632257 - 5625096 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr2 | 5625105 | 5632257 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5625105 5625302 - 5619510 1 chr1 5625105 5625302 - 5623070 2 chr2 5625105 5632257 - 5625096 df2 Chromosome Start End Strand Distance 1 chr1 5625105 5625302 - 5619510 2 chr1 5625105 5625302 - 5623070 3 chr2 5625105 5632257 - 5625096 Actual Chromosome Start End Strand Distance 0 chr1 5625105 5625302 - 5619510 1 chr1 5625105 5625302 - 5623070 2 chr2 5625105 5632257 - 5625096 Expected Chromosome Start End Strand Distance 0 chr1 5625105 5625302 - 5619510 1 chr1 5625105 5625302 - 5623070 2 chr2 5625105 5632257 - 5625096 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn8723zgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8723zgi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3747226 - 454904 1 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 4 chr1 4158022 4162240 - 875230 5 chr1 4158022 4162240 - 999525 6 chr1 4802045 4807630 + 354135 7 chr1 4802045 4807630 + 1519253 8 chr1 7165218 7172547 + 796551 9 chr1 7165218 7172547 + 1482859 10 chr1 7312411 7316991 - 652107 11 chr1 7312411 7316991 - 1338415 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4807630 | a | 0 | ... | | chr1 | 4802045 | 4807630 | a | 0 | ... | | chr1 | 3779696 | 3782240 | a | 0 | ... | | chr1 | 3779696 | 3782240 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7316991 | a | 0 | ... | | chr1 | 7312411 | 7316991 | a | 0 | ... | | chr1 | 3737696 | 3747226 | a | 0 | ... | | chr1 | 3737696 | 3747226 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3747226 - 454904 11 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 6 chr1 4158022 4162240 - 875230 7 chr1 4158022 4162240 - 999525 0 chr1 4802045 4807630 + 354135 1 chr1 4802045 4807630 + 1519253 4 chr1 7165218 7172547 + 796551 5 chr1 7165218 7172547 + 1482859 8 chr1 7312411 7316991 - 652107 9 chr1 7312411 7316991 - 1338415 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3747226 - 454904 1 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 4 chr1 4158022 4162240 - 875230 5 chr1 4158022 4162240 - 999525 6 chr1 4802045 4807630 + 354135 7 chr1 4802045 4807630 + 1519253 8 chr1 7165218 7172547 + 796551 9 chr1 7165218 7172547 + 1482859 10 chr1 7312411 7316991 - 652107 11 chr1 7312411 7316991 - 1338415 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3747226 - 454904 1 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 4 chr1 4158022 4162240 - 875230 5 chr1 4158022 4162240 - 999525 6 chr1 4802045 4807630 + 354135 7 chr1 4802045 4807630 + 1519253 8 chr1 7165218 7172547 + 796551 9 chr1 7165218 7172547 + 1482859 10 chr1 7312411 7316991 - 652107 11 chr1 7312411 7316991 - 1338415 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3747226 - 454904 1 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 4 chr1 4158022 4162240 - 875230 5 chr1 4158022 4162240 - 999525 6 chr1 4802045 4807630 + 354135 7 chr1 4802045 4807630 + 1519253 8 chr1 7165218 7172547 + 796551 9 chr1 7165218 7172547 + 1482859 10 chr1 7312411 7316991 - 652107 11 chr1 7312411 7316991 - 1338415 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpico87kom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpico87kom/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 454904 11 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 6 chr1 4158022 4161889 - 875230 7 chr1 4158022 4161889 - 999876 0 chr1 4802045 4802055 + 359710 1 chr1 4802045 4802055 + 1519253 4 chr1 7165218 7166229 + 802869 5 chr1 7165218 7166229 + 1489177 8 chr1 7312411 7313422 - 655676 9 chr1 7312411 7313422 - 1341984 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnn1kr4hh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnn1kr4hh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 454904 11 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 6 chr1 4158022 4161889 - 875230 7 chr1 4158022 4161889 - 999876 0 chr1 4802045 4802055 + 359710 1 chr1 4802045 4802055 + 1519253 4 chr1 7165218 7166229 + 802869 5 chr1 7165218 7166229 + 1489177 8 chr1 7312411 7313422 - 655676 9 chr1 7312411 7313422 - 1341984 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdu_eb19b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdu_eb19b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 2378209 1 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 4 chr1 4158022 4161889 - 2798535 5 chr1 4158022 4161889 - 4092484 6 chr1 4802045 4802055 + 3442558 7 chr1 4802045 4802055 + 4736507 8 chr1 7165218 7166229 + 5805731 9 chr1 7165218 7166229 + 7099680 10 chr1 7312411 7313422 - 5952924 11 chr1 7312411 7313422 - 7246873 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 2378209 11 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 6 chr1 4158022 4161889 - 2798535 7 chr1 4158022 4161889 - 4092484 0 chr1 4802045 4802055 + 3442558 1 chr1 4802045 4802055 + 4736507 4 chr1 7165218 7166229 + 5805731 5 chr1 7165218 7166229 + 7099680 8 chr1 7312411 7313422 - 5952924 9 chr1 7312411 7313422 - 7246873 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 2378209 1 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 4 chr1 4158022 4161889 - 2798535 5 chr1 4158022 4161889 - 4092484 6 chr1 4802045 4802055 + 3442558 7 chr1 4802045 4802055 + 4736507 8 chr1 7165218 7166229 + 5805731 9 chr1 7165218 7166229 + 7099680 10 chr1 7312411 7313422 - 5952924 11 chr1 7312411 7313422 - 7246873 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 2378209 1 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 4 chr1 4158022 4161889 - 2798535 5 chr1 4158022 4161889 - 4092484 6 chr1 4802045 4802055 + 3442558 7 chr1 4802045 4802055 + 4736507 8 chr1 7165218 7166229 + 5805731 9 chr1 7165218 7166229 + 7099680 10 chr1 7312411 7313422 - 5952924 11 chr1 7312411 7313422 - 7246873 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 2378209 1 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 4 chr1 4158022 4161889 - 2798535 5 chr1 4158022 4161889 - 4092484 6 chr1 4802045 4802055 + 3442558 7 chr1 4802045 4802055 + 4736507 8 chr1 7165218 7166229 + 5805731 9 chr1 7165218 7166229 + 7099680 10 chr1 7312411 7313422 - 5952924 11 chr1 7312411 7313422 - 7246873 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp28icy_lf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28icy_lf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 38630 1 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 4 chr1 4158022 4161889 - 377558 5 chr1 4158022 4161889 - 416956 6 chr1 4802045 4802055 + 640157 7 chr1 4802045 4802055 + 1021581 8 chr1 7165218 7166229 + 146183 9 chr1 7165218 7166229 + 2363164 10 chr1 7312411 7313422 - 146183 11 chr1 7312411 7313422 - 2510357 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 38630 11 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 6 chr1 4158022 4161889 - 377558 7 chr1 4158022 4161889 - 416956 0 chr1 4802045 4802055 + 640157 1 chr1 4802045 4802055 + 1021581 4 chr1 7165218 7166229 + 146183 5 chr1 7165218 7166229 + 2363164 8 chr1 7312411 7313422 - 146183 9 chr1 7312411 7313422 - 2510357 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 38630 1 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 4 chr1 4158022 4161889 - 377558 5 chr1 4158022 4161889 - 416956 6 chr1 4802045 4802055 + 640157 7 chr1 4802045 4802055 + 1021581 8 chr1 7165218 7166229 + 146183 9 chr1 7165218 7166229 + 2363164 10 chr1 7312411 7313422 - 146183 11 chr1 7312411 7313422 - 2510357 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 38630 1 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 4 chr1 4158022 4161889 - 377558 5 chr1 4158022 4161889 - 416956 6 chr1 4802045 4802055 + 640157 7 chr1 4802045 4802055 + 1021581 8 chr1 7165218 7166229 + 146183 9 chr1 7165218 7166229 + 2363164 10 chr1 7312411 7313422 - 146183 11 chr1 7312411 7313422 - 2510357 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 38630 1 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 4 chr1 4158022 4161889 - 377558 5 chr1 4158022 4161889 - 416956 6 chr1 4802045 4802055 + 640157 7 chr1 4802045 4802055 + 1021581 8 chr1 7165218 7166229 + 146183 9 chr1 7165218 7166229 + 2363164 10 chr1 7312411 7313422 - 146183 11 chr1 7312411 7313422 - 2510357 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpasp69p10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasp69p10/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 3737353 1 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 6 chr1 4802045 4802055 + 2793436 7 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 10 chr1 7312411 7313422 - 282069 11 chr1 7312411 7313422 - 7312068 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7165218 | 7166229 | a | 0 | ... | | chr1 | 7165218 | 7166229 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 3737353 11 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 0 chr1 4802045 4802055 + 2793436 1 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 6 chr1 7312411 7313422 - 282069 7 chr1 7312411 7313422 - 7312068 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 3737353 1 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 6 chr1 4802045 4802055 + 2793436 7 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 10 chr1 7312411 7313422 - 282069 11 chr1 7312411 7313422 - 7312068 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 3737353 1 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 6 chr1 4802045 4802055 + 2793436 7 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 10 chr1 7312411 7313422 - 282069 11 chr1 7312411 7313422 - 7312068 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 3737353 1 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 6 chr1 4802045 4802055 + 2793436 7 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 10 chr1 7312411 7313422 - 282069 11 chr1 7312411 7313422 - 7312068 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp37v968ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37v968ac/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_dftiyqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dftiyqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8613393 | 8613655 | a | 0 | ... | | chr1 | 8613393 | 8613655 | a | 0 | ... | | chr4 | 1475361 | 1475623 | a | 0 | ... | | chr4 | 1475361 | 1475623 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 df2 Chromosome Start End Strand Distance 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 Actual Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 Expected Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghy5zeaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghy5zeaa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8613393 | 8613655 | a | 0 | ... | | chr1 | 8613393 | 8613655 | a | 0 | ... | | chr4 | 1475361 | 1475623 | a | 0 | ... | | chr4 | 1475361 | 1475623 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 df2 Chromosome Start End Strand Distance 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 Actual Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 Expected Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx7tngfrc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7tngfrc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprf9t7syy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprf9t7syy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdh6mjtxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdh6mjtxo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_tyb_zs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tyb_zs5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpynhrnxl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpynhrnxl6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi9aqqn84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi9aqqn84/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 1 chr1 5369850 5372723 + 2649239 2 chr1 5496784 5501287 + 2776173 3 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4512657 | 4519206 | a | 0 | ... | | chr1 | 6679183 | 6685420 | a | 0 | ... | | chr1 | 5369850 | 5372723 | a | 0 | ... | | chr1 | 5496784 | 5501287 | a | 0 | ... | | chr1 | 6945544 | 6951253 | a | 0 | ... | | chr1 | 7707968 | 7709268 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 2 chr1 5369850 5372723 + 2649239 3 chr1 5496784 5501287 + 2776173 1 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 df2 Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 1 chr1 5369850 5372723 + 2649239 2 chr1 5496784 5501287 + 2776173 3 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 Actual Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 1 chr1 5369850 5372723 + 2649239 2 chr1 5496784 5501287 + 2776173 3 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 Expected Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 1 chr1 5369850 5372723 + 2649239 2 chr1 5496784 5501287 + 2776173 3 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjqyv3kwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqyv3kwa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 3 2 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65272 6 chr1 65537 65794 - 65519 7 chr1 5369850 5369960 - 5304304 8 chr1 5369850 5369960 - 5369585 9 chr1 6679183 6679293 - 6613637 10 chr1 6679183 6679293 - 6678918 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 111 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 7 chr1 6 116 - 3 8 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 1 chr1 65537 65794 - 65272 2 chr1 65537 65794 - 65519 9 chr1 5369850 5369960 - 5304304 10 chr1 5369850 5369960 - 5369585 5 chr1 6679183 6679293 - 6613637 6 chr1 6679183 6679293 - 6678918 df2 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 3 2 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65272 6 chr1 65537 65794 - 65519 7 chr1 5369850 5369960 - 5304304 8 chr1 5369850 5369960 - 5369585 9 chr1 6679183 6679293 - 6613637 10 chr1 6679183 6679293 - 6678918 Actual Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 3 2 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65272 6 chr1 65537 65794 - 65519 7 chr1 5369850 5369960 - 5304304 8 chr1 5369850 5369960 - 5369585 9 chr1 6679183 6679293 - 6613637 10 chr1 6679183 6679293 - 6678918 Expected Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 3 2 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65272 6 chr1 65537 65794 - 65519 7 chr1 5369850 5369960 - 5304304 8 chr1 5369850 5369960 - 5369585 9 chr1 6679183 6679293 - 6613637 10 chr1 6679183 6679293 - 6678918 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7q63jzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7q63jzi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65794 - 65280 4 chr1 5369850 5369960 - 5369593 5 chr1 6679183 6679293 - 6678926 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 6679183 | 6679293 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 2 chr1 5369850 5369960 - 5369593 1 chr1 6679183 6679293 - 6678926 df2 Chromosome Start End Strand Distance 3 chr1 65537 65794 - 65280 4 chr1 5369850 5369960 - 5369593 5 chr1 6679183 6679293 - 6678926 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 1 chr1 5369850 5369960 - 5369593 2 chr1 6679183 6679293 - 6678926 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 1 chr1 5369850 5369960 - 5369593 2 chr1 6679183 6679293 - 6678926 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwfanea8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwfanea8_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65794 - 65280 4 chr1 5369850 5369960 - 5369593 5 chr1 6679183 6679293 - 6678926 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 6679183 | 6679293 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 2 chr1 5369850 5369960 - 5369593 1 chr1 6679183 6679293 - 6678926 df2 Chromosome Start End Strand Distance 3 chr1 65537 65794 - 65280 4 chr1 5369850 5369960 - 5369593 5 chr1 6679183 6679293 - 6678926 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 1 chr1 5369850 5369960 - 5369593 2 chr1 6679183 6679293 - 6678926 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 1 chr1 5369850 5369960 - 5369593 2 chr1 6679183 6679293 - 6678926 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_yjxk5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_yjxk5n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 2 chr1 6 116 - 65422 3 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 6 chr1 65537 65794 - 65421 7 chr1 65537 65794 - 65422 8 chr1 5369850 5369960 - 1309224 9 chr1 5369850 5369960 - 5304057 10 chr1 6679183 6679293 - 1309224 11 chr1 6679183 6679293 - 6613390 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 111 | a | 0 | ... | | chr1 | 1 | 111 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 8 chr1 6 116 - 65422 9 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 2 chr1 65537 65794 - 65421 3 chr1 65537 65794 - 65422 10 chr1 5369850 5369960 - 1309224 11 chr1 5369850 5369960 - 5304057 6 chr1 6679183 6679293 - 1309224 7 chr1 6679183 6679293 - 6613390 df2 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 2 chr1 6 116 - 65422 3 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 6 chr1 65537 65794 - 65421 7 chr1 65537 65794 - 65422 8 chr1 5369850 5369960 - 1309224 9 chr1 5369850 5369960 - 5304057 10 chr1 6679183 6679293 - 1309224 11 chr1 6679183 6679293 - 6613390 Actual Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 2 chr1 6 116 - 65422 3 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 6 chr1 65537 65794 - 65421 7 chr1 65537 65794 - 65422 8 chr1 5369850 5369960 - 1309224 9 chr1 5369850 5369960 - 5304057 10 chr1 6679183 6679293 - 1309224 11 chr1 6679183 6679293 - 6613390 Expected Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 2 chr1 6 116 - 65422 3 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 6 chr1 65537 65794 - 65421 7 chr1 65537 65794 - 65422 8 chr1 5369850 5369960 - 1309224 9 chr1 5369850 5369960 - 5304057 10 chr1 6679183 6679293 - 1309224 11 chr1 6679183 6679293 - 6613390 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd0064qou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0064qou/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 6 116 - 1 2 chr1 7 117 - 1 3 chr1 7 117 - 2 4 chr1 65537 65794 - 55830 5 chr1 65537 65794 - 60945 6 chr1 5369850 5369960 - 5360143 7 chr1 5369850 5369960 - 5365258 8 chr1 6679183 6679293 - 6669476 9 chr1 6679183 6679293 - 6674591 11 chr3 9 119 - 6 12 chr9 65537 65647 - 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6679183 | 6679293 | a | 0 | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 6 116 - 1 2 chr1 7 117 - 1 3 chr1 7 117 - 2 9 chr3 9 119 - 6 10 chr9 65537 65647 - 65280 0 chr1 65537 65794 - 55830 1 chr1 65537 65794 - 60945 7 chr1 5369850 5369960 - 5360143 8 chr1 5369850 5369960 - 5365258 4 chr1 6679183 6679293 - 6669476 5 chr1 6679183 6679293 - 6674591 df2 Chromosome Start End Strand Distance 1 chr1 6 116 - 1 2 chr1 7 117 - 1 3 chr1 7 117 - 2 11 chr3 9 119 - 6 12 chr9 65537 65647 - 65280 4 chr1 65537 65794 - 55830 5 chr1 65537 65794 - 60945 6 chr1 5369850 5369960 - 5360143 7 chr1 5369850 5369960 - 5365258 8 chr1 6679183 6679293 - 6669476 9 chr1 6679183 6679293 - 6674591 Actual Chromosome Start End Strand Distance 0 chr1 6 116 - 1 1 chr1 7 117 - 1 2 chr1 7 117 - 2 3 chr1 65537 65794 - 55830 4 chr1 65537 65794 - 60945 5 chr1 5369850 5369960 - 5360143 6 chr1 5369850 5369960 - 5365258 7 chr1 6679183 6679293 - 6669476 8 chr1 6679183 6679293 - 6674591 9 chr3 9 119 - 6 10 chr9 65537 65647 - 65280 Expected Chromosome Start End Strand Distance 0 chr1 6 116 - 1 1 chr1 7 117 - 1 2 chr1 7 117 - 2 3 chr1 65537 65794 - 55830 4 chr1 65537 65794 - 60945 5 chr1 5369850 5369960 - 5360143 6 chr1 5369850 5369960 - 5365258 7 chr1 6679183 6679293 - 6669476 8 chr1 6679183 6679293 - 6674591 9 chr3 9 119 - 6 10 chr9 65537 65647 - 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmiw_38n5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmiw_38n5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 5 2 chr1 6 116 - 65422 3 chr1 7 117 - 6 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65536 6 chr1 5369850 5369960 - 5304307 7 chr1 5369850 5369960 - 5369849 8 chr1 6679183 6679293 - 6613640 9 chr1 6679183 6679293 - 6679182 11 chr3 9 119 - 8 12 chr9 65537 65647 - 65536 13 chrM 7 117 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 111 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 6 chr1 6 116 - 5 7 chr1 6 116 - 65422 2 chr1 7 117 - 6 12 chrM 7 117 - 6 3 chr1 7 117 - 65421 10 chr3 9 119 - 8 11 chr9 65537 65647 - 65536 1 chr1 65537 65794 - 65536 8 chr1 5369850 5369960 - 5304307 9 chr1 5369850 5369960 - 5369849 4 chr1 6679183 6679293 - 6613640 5 chr1 6679183 6679293 - 6679182 df2 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 5 2 chr1 6 116 - 65422 3 chr1 7 117 - 6 13 chrM 7 117 - 6 4 chr1 7 117 - 65421 11 chr3 9 119 - 8 12 chr9 65537 65647 - 65536 5 chr1 65537 65794 - 65536 6 chr1 5369850 5369960 - 5304307 7 chr1 5369850 5369960 - 5369849 8 chr1 6679183 6679293 - 6613640 9 chr1 6679183 6679293 - 6679182 Actual Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 5 2 chr1 6 116 - 65422 3 chr1 7 117 - 6 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65536 6 chr1 5369850 5369960 - 5304307 7 chr1 5369850 5369960 - 5369849 8 chr1 6679183 6679293 - 6613640 9 chr1 6679183 6679293 - 6679182 10 chr3 9 119 - 8 11 chr9 65537 65647 - 65536 12 chrM 7 117 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 5 2 chr1 6 116 - 65422 3 chr1 7 117 - 6 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65536 6 chr1 5369850 5369960 - 5304307 7 chr1 5369850 5369960 - 5369849 8 chr1 6679183 6679293 - 6613640 9 chr1 6679183 6679293 - 6679182 10 chr3 9 119 - 8 11 chr9 65537 65647 - 65536 12 chrM 7 117 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbtrw3hi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbtrw3hi6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 460608 - 2130996 1 chr1 450608 460608 - 9088653 2 chr1 1644931 1654931 + 936673 3 chr1 1644931 1654931 + 7894330 4 chr1 4588101 4598101 - 1993499 5 chr1 4588101 4598101 - 4951160 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 450608 460608 - 2130996 5 chr1 450608 460608 - 9088653 0 chr1 1644931 1654931 + 936673 1 chr1 1644931 1654931 + 7894330 2 chr1 4588101 4598101 - 1993499 3 chr1 4588101 4598101 - 4951160 df2 Chromosome Start End Strand Distance 0 chr1 450608 460608 - 2130996 1 chr1 450608 460608 - 9088653 2 chr1 1644931 1654931 + 936673 3 chr1 1644931 1654931 + 7894330 4 chr1 4588101 4598101 - 1993499 5 chr1 4588101 4598101 - 4951160 Actual Chromosome Start End Strand Distance 0 chr1 450608 460608 - 2130996 1 chr1 450608 460608 - 9088653 2 chr1 1644931 1654931 + 936673 3 chr1 1644931 1654931 + 7894330 4 chr1 4588101 4598101 - 1993499 5 chr1 4588101 4598101 - 4951160 Expected Chromosome Start End Strand Distance 0 chr1 450608 460608 - 2130996 1 chr1 450608 460608 - 9088653 2 chr1 1644931 1654931 + 936673 3 chr1 1644931 1654931 + 7894330 4 chr1 4588101 4598101 - 1993499 5 chr1 4588101 4598101 - 4951160 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvk9n4ff2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvk9n4ff2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 460608 - 444910 0 chr1 1644931 1654931 + 1639233 1 chr1 4588101 4598101 - 4582403 df2 Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Expected Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4mm4_07w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mm4_07w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 460608 - 444910 0 chr1 1644931 1654931 + 1639233 1 chr1 4588101 4598101 - 4582403 df2 Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Expected Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptlr2xc88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlr2xc88/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 460608 - 444910 0 chr1 1644931 1654931 + 1639233 1 chr1 4588101 4598101 - 4582403 df2 Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Expected Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7kbw3z5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7kbw3z5w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4588101 | 4588104 | a | 0 | ... | | chr1 | 4588101 | 4588104 | a | 0 | ... | | chr1 | 450608 | 450865 | a | 0 | ... | | chr1 | 450608 | 450865 | a | 0 | ... | | chr1 | 1644931 | 1644933 | a | 0 | ... | | chr1 | 1644931 | 1644933 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 450865 - 450597 3 chr1 450608 450865 - 2158496 4 chr1 1644931 1644933 - 964428 5 chr1 1644931 1644933 - 1644920 0 chr1 4588101 4588104 - 1978741 1 chr1 4588101 4588104 - 4588090 df2 Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Actual Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Expected Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcxiyvtrs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxiyvtrs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4588101 | 4588104 | a | 0 | ... | | chr1 | 4588101 | 4588104 | a | 0 | ... | | chr1 | 450608 | 450865 | a | 0 | ... | | chr1 | 450608 | 450865 | a | 0 | ... | | chr1 | 1644931 | 1644933 | a | 0 | ... | | chr1 | 1644931 | 1644933 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 450865 - 450597 3 chr1 450608 450865 - 2158496 4 chr1 1644931 1644933 - 964428 5 chr1 1644931 1644933 - 1644920 0 chr1 4588101 4588104 - 1978741 1 chr1 4588101 4588104 - 4588090 df2 Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Actual Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Expected Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvthhnmg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvthhnmg_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr2 1 3 - 9 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 3 - 9 df2 Chromosome Start End Strand Distance 3 chr2 1 3 - 9 Actual Chromosome Start End Strand Distance 0 chr2 1 3 - 9 Expected Chromosome Start End Strand Distance 0 chr2 1 3 - 9 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxcrcu0zb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcrcu0zb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 6273276 1 chr1 1585214 1587914 - 8082640 2 chr1 2087956 2095084 - 5766106 3 chr1 2087956 2095084 - 7575470 4 chr1 7414117 7423198 - 437992 5 chr1 7414117 7423198 - 2247356 6 chr19 3302345 3308284 - 1772474 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2087956 | 2095084 | a | 0 | ... | | chr1 | 2087956 | 2095084 | a | 0 | ... | | chr1 | 7414117 | 7423198 | a | 0 | ... | | chr1 | 7414117 | 7423198 | a | 0 | ... | | chr1 | 1585214 | 1587914 | a | 0 | ... | | chr1 | 1585214 | 1587914 | a | 0 | ... | | chr19 | 3302345 | 3308284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1585214 1587914 - 6273276 5 chr1 1585214 1587914 - 8082640 0 chr1 2087956 2095084 - 5766106 1 chr1 2087956 2095084 - 7575470 6 chr19 3302345 3308284 - 1772474 2 chr1 7414117 7423198 - 437992 3 chr1 7414117 7423198 - 2247356 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 6273276 1 chr1 1585214 1587914 - 8082640 2 chr1 2087956 2095084 - 5766106 3 chr1 2087956 2095084 - 7575470 6 chr19 3302345 3308284 - 1772474 4 chr1 7414117 7423198 - 437992 5 chr1 7414117 7423198 - 2247356 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 6273276 1 chr1 1585214 1587914 - 8082640 2 chr1 2087956 2095084 - 5766106 3 chr1 2087956 2095084 - 7575470 4 chr1 7414117 7423198 - 437992 5 chr1 7414117 7423198 - 2247356 6 chr19 3302345 3308284 - 1772474 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 6273276 1 chr1 1585214 1587914 - 8082640 2 chr1 2087956 2095084 - 5766106 3 chr1 2087956 2095084 - 7575470 4 chr1 7414117 7423198 - 437992 5 chr1 7414117 7423198 - 2247356 6 chr19 3302345 3308284 - 1772474 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6u_zqlx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6u_zqlx0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2087956 | 2095084 | a | 0 | ... | | chr1 | 7414117 | 7423198 | a | 0 | ... | | chr1 | 1585214 | 1587914 | a | 0 | ... | | chr19 | 3302345 | 3308284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1585214 1587914 - 1584952 0 chr1 2087956 2095084 - 2087694 3 chr19 3302345 3308284 - 3302083 1 chr1 7414117 7423198 - 7413855 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 3 chr19 3302345 3308284 - 3302083 2 chr1 7414117 7423198 - 7413855 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjh5d42qj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh5d42qj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2087956 | 2095084 | a | 0 | ... | | chr1 | 7414117 | 7423198 | a | 0 | ... | | chr1 | 1585214 | 1587914 | a | 0 | ... | | chr19 | 3302345 | 3308284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1585214 1587914 - 1584952 0 chr1 2087956 2095084 - 2087694 3 chr19 3302345 3308284 - 3302083 1 chr1 7414117 7423198 - 7413855 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 3 chr19 3302345 3308284 - 3302083 2 chr1 7414117 7423198 - 7413855 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1upyokfo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1upyokfo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr19 3302345 3308284 - 3302083 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr19 | 3302345 | 3308284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr19 3302345 3308284 - 3302083 df2 Chromosome Start End Strand Distance 3 chr19 3302345 3308284 - 3302083 Actual Chromosome Start End Strand Distance 0 chr19 3302345 3308284 - 3302083 Expected Chromosome Start End Strand Distance 0 chr19 3302345 3308284 - 3302083 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnsj8sg_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnsj8sg_6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7414117 | 7414219 | a | 0 | ... | | chr1 | 1585214 | 1585215 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1585214 1585215 - 1519631 0 chr1 7414117 7414219 - 7348534 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk2ut607w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2ut607w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7414117 | 7414219 | a | 0 | ... | | chr1 | 1585214 | 1585215 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1585214 1585215 - 1519631 0 chr1 7414117 7414219 - 7348534 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgtxn_hkj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgtxn_hkj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1585215 + 1519631 1 chr1 7414117 7414219 + 7348534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7414117 | 7414219 | a | 0 | ... | | chr1 | 1585214 | 1585215 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1585214 1585215 + 1519631 0 chr1 7414117 7414219 + 7348534 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1585215 + 1519631 1 chr1 7414117 7414219 + 7348534 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1585215 + 1519631 1 chr1 7414117 7414219 + 7348534 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1585215 + 1519631 1 chr1 7414117 7414219 + 7348534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7p518_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7p518_l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 159458 1 chr1 3523727 3530748 - 1108129 2 chr1 6765373 6765374 - 191412 3 chr1 6765373 6765374 - 192832 4 chr1 6765373 6767936 + 191412 5 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 10 chr1 6765373 6775211 + 191412 11 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6765373 | 6767936 | a | 0 | ... | | chr1 | 6765373 | 6767936 | a | 0 | ... | | chr1 | 6765373 | 6775211 | a | 0 | ... | | chr1 | 6765373 | 6775211 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6765373 | 6773593 | a | 0 | ... | | chr1 | 6765373 | 6773593 | a | 0 | ... | | chr1 | 3523727 | 3530748 | a | 0 | ... | | chr1 | 3523727 | 3530748 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3523727 3530748 - 159458 11 chr1 3523727 3530748 - 1108129 4 chr1 6765373 6765374 - 191412 5 chr1 6765373 6765374 - 192832 0 chr1 6765373 6767936 + 191412 1 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 2 chr1 6765373 6775211 + 191412 3 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 df2 Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 159458 1 chr1 3523727 3530748 - 1108129 2 chr1 6765373 6765374 - 191412 3 chr1 6765373 6765374 - 192832 4 chr1 6765373 6767936 + 191412 5 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 10 chr1 6765373 6775211 + 191412 11 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 Actual Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 159458 1 chr1 3523727 3530748 - 1108129 2 chr1 6765373 6765374 - 191412 3 chr1 6765373 6765374 - 192832 4 chr1 6765373 6767936 + 191412 5 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 10 chr1 6765373 6775211 + 191412 11 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 Expected Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 159458 1 chr1 3523727 3530748 - 1108129 2 chr1 6765373 6765374 - 191412 3 chr1 6765373 6765374 - 192832 4 chr1 6765373 6767936 + 191412 5 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 10 chr1 6765373 6775211 + 191412 11 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnf0embpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnf0embpi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 5 chr1 6765373 6775211 + 3234626 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6765373 | 6767936 | a | 0 | ... | | chr1 | 6765373 | 6775211 | a | 0 | ... | | chr1 | 6765373 | 6765374 | a | 0 | ... | | chr1 | 6765373 | 6771834 | a | 0 | ... | | chr1 | 6765373 | 6773593 | a | 0 | ... | | chr1 | 3523727 | 3530748 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 3523727 3530748 - 3234626 2 chr1 6765373 6765374 - 3234626 0 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 1 chr1 6765373 6775211 + 3234626 df2 Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 5 chr1 6765373 6775211 + 3234626 Actual Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 5 chr1 6765373 6775211 + 3234626 Expected Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 5 chr1 6765373 6775211 + 3234626 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyxgewsan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyxgewsan/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 + 3234626 5 chr1 6765373 6775211 + 3234626 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6765373 | 6767936 | a | 0 | ... | | chr1 | 6765373 | 6773593 | a | 0 | ... | | chr1 | 6765373 | 6775211 | a | 0 | ... | | chr1 | 6765373 | 6765374 | a | 0 | ... | | chr1 | 6765373 | 6771834 | a | 0 | ... | | chr1 | 3523727 | 3530748 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 3523727 3530748 - 3234626 3 chr1 6765373 6765374 - 3234626 0 chr1 6765373 6767936 + 3234626 4 chr1 6765373 6771834 - 3234626 1 chr1 6765373 6773593 + 3234626 2 chr1 6765373 6775211 + 3234626 df2 Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 + 3234626 5 chr1 6765373 6775211 + 3234626 Actual Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 + 3234626 5 chr1 6765373 6775211 + 3234626 Expected Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 + 3234626 5 chr1 6765373 6775211 + 3234626 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0eog34v_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0eog34v_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 0 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpke0yoxmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpke0yoxmb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 0 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp6yfl9hd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6yfl9hd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65515 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 0 chr1 65537 65794 - 65515 df2 Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65515 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65515 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65515 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppngq285x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppngq285x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65533 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 0 chr1 65537 65794 - 65533 df2 Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65533 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65533 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm5iduuwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5iduuwd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 451624 1 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 4 chr1 8594171 8604156 + 731414 5 chr1 8594171 8604156 + 1322949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1502864 1507072 - 451624 5 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 0 chr1 8594171 8604156 + 731414 1 chr1 8594171 8604156 + 1322949 df2 Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 451624 1 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 4 chr1 8594171 8604156 + 731414 5 chr1 8594171 8604156 + 1322949 Actual Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 451624 1 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 4 chr1 8594171 8604156 + 731414 5 chr1 8594171 8604156 + 1322949 Expected Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 451624 1 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 4 chr1 8594171 8604156 + 731414 5 chr1 8594171 8604156 + 1322949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdo3wxhif/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdo3wxhif/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 5061998 1 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 4 chr1 8594171 8604156 + 2016902 5 chr1 8594171 8604156 + 7087100 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1502864 1507072 - 5061998 5 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 0 chr1 8594171 8604156 + 2016902 1 chr1 8594171 8604156 + 7087100 df2 Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 5061998 1 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 4 chr1 8594171 8604156 + 2016902 5 chr1 8594171 8604156 + 7087100 Actual Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 5061998 1 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 4 chr1 8594171 8604156 + 2016902 5 chr1 8594171 8604156 + 7087100 Expected Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 5061998 1 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 4 chr1 8594171 8604156 + 2016902 5 chr1 8594171 8604156 + 7087100 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6znkwv3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6znkwv3p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 1437326 1 chr1 1502864 1507072 - 1502858 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 4 chr1 8594171 8604156 + 8528633 5 chr1 8594171 8604156 + 8594165 8 chr20 4644978 4649186 - 4644972 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | | chr20 | 4644978 | 4649186 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1502864 1507072 - 1437326 5 chr1 1502864 1507072 - 1502858 6 chr20 4644978 4649186 - 4644972 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 0 chr1 8594171 8604156 + 8528633 1 chr1 8594171 8604156 + 8594165 df2 Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 1437326 1 chr1 1502864 1507072 - 1502858 8 chr20 4644978 4649186 - 4644972 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 4 chr1 8594171 8604156 + 8528633 5 chr1 8594171 8604156 + 8594165 Actual Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 1437326 1 chr1 1502864 1507072 - 1502858 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 4 chr1 8594171 8604156 + 8528633 5 chr1 8594171 8604156 + 8594165 6 chr20 4644978 4649186 - 4644972 Expected Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 1437326 1 chr1 1502864 1507072 - 1502858 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 4 chr1 8594171 8604156 + 8528633 5 chr1 8594171 8604156 + 8594165 6 chr20 4644978 4649186 - 4644972 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyar99xpf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyar99xpf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65532 2 chr1 65537 65539 - 65533 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2 7 - 65531 0 chr1 65537 65539 - 65532 1 chr1 65537 65539 - 65533 df2 Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65532 2 chr1 65537 65539 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65532 2 chr1 65537 65539 - 65533 Expected Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65532 2 chr1 65537 65539 - 65533 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4e715zxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4e715zxo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2 7 - 65531 0 chr1 65537 65539 - 65531 df2 Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq3mw8eyb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3mw8eyb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65794 + 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 + 65280 df2 Chromosome Start End Strand Distance 3 chr1 65537 65794 + 65280 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 + 65280 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 + 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8rq4ahr_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8rq4ahr_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfy5nqfs8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfy5nqfs8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl1xumotk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl1xumotk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp957rtx1r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp957rtx1r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgw73l8eo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgw73l8eo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptu4_9tyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptu4_9tyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2y5tuvje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2y5tuvje/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10 | 16 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 df2 Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 Actual Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 Expected Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuzedo8c6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuzedo8c6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdt3c6xhn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt3c6xhn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 379353 1 chr1 5631745 5640565 - 2097758 2 chr1 5631745 5640565 - 2098709 3 chr1 8861813 8870991 - 5327826 4 chr1 8861813 8870991 - 5328777 5 chr1 9881162 9884464 - 6347175 6 chr1 9881162 9884464 - 6348126 7 chr1 9881162 9887404 + 6347175 8 chr1 9881162 9887404 + 6348126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | chr1 | 3144471 | 3146364 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 3144471 3146364 - 379353 2 chr1 5631745 5640565 - 2097758 3 chr1 5631745 5640565 - 2098709 7 chr1 8861813 8870991 - 5327826 8 chr1 8861813 8870991 - 5328777 4 chr1 9881162 9884464 - 6347175 5 chr1 9881162 9884464 - 6348126 0 chr1 9881162 9887404 + 6347175 1 chr1 9881162 9887404 + 6348126 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 379353 1 chr1 5631745 5640565 - 2097758 2 chr1 5631745 5640565 - 2098709 3 chr1 8861813 8870991 - 5327826 4 chr1 8861813 8870991 - 5328777 5 chr1 9881162 9884464 - 6347175 6 chr1 9881162 9884464 - 6348126 7 chr1 9881162 9887404 + 6347175 8 chr1 9881162 9887404 + 6348126 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 379353 1 chr1 5631745 5640565 - 2097758 2 chr1 5631745 5640565 - 2098709 3 chr1 8861813 8870991 - 5327826 4 chr1 8861813 8870991 - 5328777 5 chr1 9881162 9884464 - 6347175 6 chr1 9881162 9884464 - 6348126 7 chr1 9881162 9887404 + 6347175 8 chr1 9881162 9887404 + 6348126 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 379353 1 chr1 5631745 5640565 - 2097758 2 chr1 5631745 5640565 - 2098709 3 chr1 8861813 8870991 - 5327826 4 chr1 8861813 8870991 - 5328777 5 chr1 9881162 9884464 - 6347175 6 chr1 9881162 9884464 - 6348126 7 chr1 9881162 9887404 + 6347175 8 chr1 9881162 9887404 + 6348126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpln34suwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpln34suwx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 + 1010172 9 chr1 9881162 9887404 + 4240598 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3144471 | 3146364 | a | 0 | ... | | chr1 | 3144471 | 3146364 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 3144471 3146364 - 2485382 7 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 8 chr1 8861813 8870991 - 1010172 9 chr1 8861813 8870991 - 3221249 4 chr1 9881162 9884464 - 1010172 5 chr1 9881162 9884464 - 4240598 0 chr1 9881162 9887404 + 1010172 1 chr1 9881162 9887404 + 4240598 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 + 1010172 9 chr1 9881162 9887404 + 4240598 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 + 1010172 9 chr1 9881162 9887404 + 4240598 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 + 1010172 9 chr1 9881162 9887404 + 4240598 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjra8ep6z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjra8ep6z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 3078934 1 chr1 3144471 3146364 - 3144459 2 chr1 5631745 5640565 + 5566208 3 chr1 5631745 5640565 + 5631733 4 chr1 8861813 8870991 - 8796276 5 chr1 8861813 8870991 - 8861801 6 chr1 9881162 9884464 - 9815625 7 chr1 9881162 9884464 - 9881150 8 chr1 9881162 9887404 - 9815625 9 chr1 9881162 9887404 - 9881150 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 3144471 3146364 - 3078934 5 chr1 3144471 3146364 - 3144459 0 chr1 5631745 5640565 + 5566208 1 chr1 5631745 5640565 + 5631733 8 chr1 8861813 8870991 - 8796276 9 chr1 8861813 8870991 - 8861801 2 chr1 9881162 9884464 - 9815625 3 chr1 9881162 9884464 - 9881150 6 chr1 9881162 9887404 - 9815625 7 chr1 9881162 9887404 - 9881150 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 3078934 1 chr1 3144471 3146364 - 3144459 2 chr1 5631745 5640565 + 5566208 3 chr1 5631745 5640565 + 5631733 4 chr1 8861813 8870991 - 8796276 5 chr1 8861813 8870991 - 8861801 6 chr1 9881162 9884464 - 9815625 7 chr1 9881162 9884464 - 9881150 8 chr1 9881162 9887404 - 9815625 9 chr1 9881162 9887404 - 9881150 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 3078934 1 chr1 3144471 3146364 - 3144459 2 chr1 5631745 5640565 + 5566208 3 chr1 5631745 5640565 + 5631733 4 chr1 8861813 8870991 - 8796276 5 chr1 8861813 8870991 - 8861801 6 chr1 9881162 9884464 - 9815625 7 chr1 9881162 9884464 - 9881150 8 chr1 9881162 9887404 - 9815625 9 chr1 9881162 9887404 - 9881150 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 3078934 1 chr1 3144471 3146364 - 3144459 2 chr1 5631745 5640565 + 5566208 3 chr1 5631745 5640565 + 5631733 4 chr1 8861813 8870991 - 8796276 5 chr1 8861813 8870991 - 8861801 6 chr1 9881162 9884464 - 9815625 7 chr1 9881162 9884464 - 9881150 8 chr1 9881162 9887404 - 9815625 9 chr1 9881162 9887404 - 9881150 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5opxkvy4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5opxkvy4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 + 2485382 3 chr1 5631745 5640565 + 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 - 1010172 9 chr1 9881162 9887404 - 4240598 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 3144471 3146364 - 2485382 5 chr1 3144471 3146364 - 5715450 0 chr1 5631745 5640565 + 2485382 1 chr1 5631745 5640565 + 3221249 8 chr1 8861813 8870991 - 1010172 9 chr1 8861813 8870991 - 3221249 2 chr1 9881162 9884464 - 1010172 3 chr1 9881162 9884464 - 4240598 6 chr1 9881162 9887404 - 1010172 7 chr1 9881162 9887404 - 4240598 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 + 2485382 3 chr1 5631745 5640565 + 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 - 1010172 9 chr1 9881162 9887404 - 4240598 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 + 2485382 3 chr1 5631745 5640565 + 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 - 1010172 9 chr1 9881162 9887404 - 4240598 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 + 2485382 3 chr1 5631745 5640565 + 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 - 1010172 9 chr1 9881162 9887404 - 4240598 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9c4xtuw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9c4xtuw4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 4 chr1 9881162 9881419 - 9880903 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5632002 | a | 0 | ... | | chr1 | 9881162 | 9881419 | a | 0 | ... | | chr1 | 3144471 | 3144728 | a | 0 | ... | | chr1 | 9881162 | 9881419 | a | 0 | ... | | chr1 | 8861813 | 8862070 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3144471 3144728 - 3144212 0 chr1 5631745 5632002 - 5631486 4 chr1 8861813 8862070 - 8861554 1 chr1 9881162 9881419 - 9880903 3 chr1 9881162 9881419 - 9880903 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 4 chr1 9881162 9881419 - 9880903 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 4 chr1 9881162 9881419 - 9880903 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 4 chr1 9881162 9881419 - 9880903 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuk_96f9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuk_96f9s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5632002 | a | 0 | ... | | chr1 | 3144471 | 3144728 | a | 0 | ... | | chr1 | 9881162 | 9881419 | a | 0 | ... | | chr1 | 8861813 | 8862070 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3144471 3144728 - 3144212 0 chr1 5631745 5632002 - 5631486 3 chr1 8861813 8862070 - 8861554 2 chr1 9881162 9881419 - 9880903 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsas9u5ve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsas9u5ve/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5632002 | a | 0 | ... | | chr1 | 3144471 | 3144728 | a | 0 | ... | | chr1 | 9881162 | 9881419 | a | 0 | ... | | chr1 | 8861813 | 8862070 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3144471 3144728 - 3144212 0 chr1 5631745 5632002 - 5631486 3 chr1 8861813 8862070 - 8861554 2 chr1 9881162 9881419 - 9880903 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzkhqfrjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzkhqfrjh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 2954 - 4194650 1 chr1 2 2954 - 8439305 2 chr1 698738 701690 + 3495914 3 chr1 698738 701690 + 7740569 4 chr1 2481278 2491278 - 1706326 5 chr1 2481278 2491278 - 5950981 6 chr1 7407375 7410327 - 1031932 7 chr1 7407375 7410327 - 3206855 8 chr1 9413409 9418115 - 967928 9 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 16 chrY 1913264 1913266 - 702332 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 698738 | 701690 | a | 0 | ... | | chr1 | 698738 | 701690 | a | 0 | ... | | chr1 | 2481278 | 2491278 | a | 0 | ... | | chr1 | 2481278 | 2491278 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7407375 | 7410327 | a | 0 | ... | | chr1 | 7407375 | 7410327 | a | 0 | ... | | chr1 | 9444205 | 9447157 | a | 0 | ... | | chr1 | 9444205 | 9447157 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 2954 - 4194650 5 chr1 2 2954 - 8439305 0 chr1 698738 701690 + 3495914 1 chr1 698738 701690 + 7740569 12 chrY 1913264 1913266 - 702332 2 chr1 2481278 2491278 - 1706326 3 chr1 2481278 2491278 - 5950981 8 chr1 7407375 7410327 - 1031932 9 chr1 7407375 7410327 - 3206855 6 chr1 9413409 9418115 - 967928 7 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 df2 Chromosome Start End Strand Distance 0 chr1 2 2954 - 4194650 1 chr1 2 2954 - 8439305 2 chr1 698738 701690 + 3495914 3 chr1 698738 701690 + 7740569 16 chrY 1913264 1913266 - 702332 4 chr1 2481278 2491278 - 1706326 5 chr1 2481278 2491278 - 5950981 6 chr1 7407375 7410327 - 1031932 7 chr1 7407375 7410327 - 3206855 8 chr1 9413409 9418115 - 967928 9 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 Actual Chromosome Start End Strand Distance 0 chr1 2 2954 - 4194650 1 chr1 2 2954 - 8439305 2 chr1 698738 701690 + 3495914 3 chr1 698738 701690 + 7740569 4 chr1 2481278 2491278 - 1706326 5 chr1 2481278 2491278 - 5950981 6 chr1 7407375 7410327 - 1031932 7 chr1 7407375 7410327 - 3206855 8 chr1 9413409 9418115 - 967928 9 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 12 chrY 1913264 1913266 - 702332 Expected Chromosome Start End Strand Distance 0 chr1 2 2954 - 4194650 1 chr1 2 2954 - 8439305 2 chr1 698738 701690 + 3495914 3 chr1 698738 701690 + 7740569 4 chr1 2481278 2491278 - 1706326 5 chr1 2481278 2491278 - 5950981 6 chr1 7407375 7410327 - 1031932 7 chr1 7407375 7410327 - 3206855 8 chr1 9413409 9418115 - 967928 9 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 12 chrY 1913264 1913266 - 702332 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvwbp267i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwbp267i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 698738 701690 - 698481 2 chr1 2481278 2491278 - 2481021 3 chr1 7407375 7410327 + 7407118 4 chr1 9413409 9418115 + 9413152 5 chr1 9444205 9447157 - 9443948 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9413409 | 9418115 | a | 0 | ... | | chr1 | 7407375 | 7410327 | a | 0 | ... | | chr1 | 2481278 | 2491278 | a | 0 | ... | | chr1 | 698738 | 701690 | a | 0 | ... | | chr1 | 9444205 | 9447157 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 698738 701690 - 698481 2 chr1 2481278 2491278 - 2481021 1 chr1 7407375 7410327 + 7407118 0 chr1 9413409 9418115 + 9413152 4 chr1 9444205 9447157 - 9443948 df2 Chromosome Start End Strand Distance 1 chr1 698738 701690 - 698481 2 chr1 2481278 2491278 - 2481021 3 chr1 7407375 7410327 + 7407118 4 chr1 9413409 9418115 + 9413152 5 chr1 9444205 9447157 - 9443948 Actual Chromosome Start End Strand Distance 0 chr1 698738 701690 - 698481 1 chr1 2481278 2491278 - 2481021 2 chr1 7407375 7410327 + 7407118 3 chr1 9413409 9418115 + 9413152 4 chr1 9444205 9447157 - 9443948 Expected Chromosome Start End Strand Distance 0 chr1 698738 701690 - 698481 1 chr1 2481278 2491278 - 2481021 2 chr1 7407375 7410327 + 7407118 3 chr1 9413409 9418115 + 9413152 4 chr1 9444205 9447157 - 9443948 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwxzoxbkf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxzoxbkf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 2954 - 1910311 1 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 3 chr1 7407375 7410327 + 5493855 4 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9413409 | 9418115 | a | 0 | ... | | chr1 | 7407375 | 7410327 | a | 0 | ... | | chr1 | 2481278 | 2491278 | a | 0 | ... | | chr1 | 698738 | 701690 | a | 0 | ... | | chr1 | 2 | 2954 | a | 0 | ... | | chr1 | 9444205 | 9447157 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 2954 - 1910311 3 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 1 chr1 7407375 7410327 + 5493855 0 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 df2 Chromosome Start End Strand Distance 0 chr1 2 2954 - 1910311 1 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 3 chr1 7407375 7410327 + 5493855 4 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 Actual Chromosome Start End Strand Distance 0 chr1 2 2954 - 1910311 1 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 3 chr1 7407375 7410327 + 5493855 4 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 Expected Chromosome Start End Strand Distance 0 chr1 2 2954 - 1910311 1 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 3 chr1 7407375 7410327 + 5493855 4 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3ys96l2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3ys96l2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 65537 65794 - 65278 5 chr1 65537 65794 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 df2 Chromosome Start End Strand Distance 4 chr1 65537 65794 - 65278 5 chr1 65537 65794 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxlfaz_i7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlfaz_i7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 65537 65794 - 65278 5 chr1 65537 65794 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 df2 Chromosome Start End Strand Distance 4 chr1 65537 65794 - 65278 5 chr1 65537 65794 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpupx3cmqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupx3cmqm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 261 - 65277 1 chr1 4 261 - 65277 2 chr1 4 5 - 65533 3 chr1 4 9 - 65529 4 chr1 65537 65794 - 65277 5 chr1 65537 65794 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 4 | 261 | a | 0 | ... | | chr1 | 4 | 9 | a | 0 | ... | | chr1 | 4 | 261 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 4 5 - 65533 3 chr1 4 9 - 65529 2 chr1 4 261 - 65277 4 chr1 4 261 - 65277 0 chr1 65537 65794 - 65277 1 chr1 65537 65794 - 65531 df2 Chromosome Start End Strand Distance 2 chr1 4 5 - 65533 3 chr1 4 9 - 65529 0 chr1 4 261 - 65277 1 chr1 4 261 - 65277 4 chr1 65537 65794 - 65277 5 chr1 65537 65794 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr1 4 261 - 65277 3 chr1 4 261 - 65277 4 chr1 65537 65794 - 65277 5 chr1 65537 65794 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr1 4 261 - 65277 3 chr1 4 261 - 65277 4 chr1 65537 65794 - 65277 5 chr1 65537 65794 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8sbnootx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8sbnootx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 261 - 65277 1 chr1 4 261 - 65277 2 chr1 4 5 - 65533 3 chr1 4 9 - 65529 6 chr2 4 261 - 65277 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | | chr1 | 4 | 9 | a | 0 | ... | | chr1 | 4 | 261 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr2 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 4 5 - 65533 1 chr1 4 9 - 65529 0 chr1 4 261 - 65277 2 chr1 4 261 - 65277 4 chr2 4 261 - 65277 df2 Chromosome Start End Strand Distance 2 chr1 4 5 - 65533 3 chr1 4 9 - 65529 0 chr1 4 261 - 65277 1 chr1 4 261 - 65277 6 chr2 4 261 - 65277 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr1 4 261 - 65277 3 chr1 4 261 - 65277 4 chr2 4 261 - 65277 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr1 4 261 - 65277 3 chr1 4 261 - 65277 4 chr2 4 261 - 65277 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp082usoju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp082usoju/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1345654 1352455 + 69202 1 chr1 1345654 1352455 + 93559 2 chr1 2356401 2365769 + 443297 3 chr1 2356401 2365769 + 928153 4 chr1 7085902 7095901 + 1533288 5 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2356401 | 2365769 | a | 0 | ... | | chr1 | 2356401 | 2365769 | a | 0 | ... | | chr1 | 7085902 | 7095901 | a | 0 | ... | | chr1 | 7085902 | 7095901 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8473657 | 8480066 | a | 0 | ... | | chr1 | 8473657 | 8480066 | a | 0 | ... | | chr1 | 10000000 | 10004190 | a | 0 | ... | | chr1 | 10000000 | 10004190 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1345654 1352455 + 69202 5 chr1 1345654 1352455 + 93559 0 chr1 2356401 2365769 + 443297 1 chr1 2356401 2365769 + 928153 2 chr1 7085902 7095901 + 1533288 3 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 df2 Chromosome Start End Strand Distance 0 chr1 1345654 1352455 + 69202 1 chr1 1345654 1352455 + 93559 2 chr1 2356401 2365769 + 443297 3 chr1 2356401 2365769 + 928153 4 chr1 7085902 7095901 + 1533288 5 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 Actual Chromosome Start End Strand Distance 0 chr1 1345654 1352455 + 69202 1 chr1 1345654 1352455 + 93559 2 chr1 2356401 2365769 + 443297 3 chr1 2356401 2365769 + 928153 4 chr1 7085902 7095901 + 1533288 5 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 Expected Chromosome Start End Strand Distance 0 chr1 1345654 1352455 + 69202 1 chr1 1345654 1352455 + 93559 2 chr1 2356401 2365769 + 443297 3 chr1 2356401 2365769 + 928153 4 chr1 7085902 7095901 + 1533288 5 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1qdoiqzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qdoiqzf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1297 + 29071 1 chr1 1 1297 + 1247562 2 chr1 30367 33219 - 29071 3 chr1 30367 33219 - 1215640 4 chr1 1248858 1252096 + 169561 5 chr1 1248858 1252096 + 1215640 6 chr1 1421656 1428249 + 169561 7 chr1 1421656 1428249 + 1380817 8 chr1 2809065 2809560 + 1380817 9 chr1 2809065 2809560 + 1556970 10 chr1 8629188 8632609 + 1239722 11 chr1 8629188 8632609 + 5819629 12 chr1 9872330 9876536 + 1239722 13 chr1 9872330 9876536 + 7062771 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1421656 | 1428249 | a | 0 | ... | | chr1 | 1421656 | 1428249 | a | 0 | ... | | chr1 | 2809065 | 2809560 | a | 0 | ... | | chr1 | 2809065 | 2809560 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9872330 | 9876536 | a | 0 | ... | | chr1 | 9872330 | 9876536 | a | 0 | ... | | chr1 | 30367 | 33219 | a | 0 | ... | | chr1 | 30367 | 33219 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 1297 + 29071 5 chr1 1 1297 + 1247562 12 chr1 30367 33219 - 29071 13 chr1 30367 33219 - 1215640 8 chr1 1248858 1252096 + 169561 9 chr1 1248858 1252096 + 1215640 0 chr1 1421656 1428249 + 169561 1 chr1 1421656 1428249 + 1380817 2 chr1 2809065 2809560 + 1380817 3 chr1 2809065 2809560 + 1556970 6 chr1 8629188 8632609 + 1239722 7 chr1 8629188 8632609 + 5819629 10 chr1 9872330 9876536 + 1239722 11 chr1 9872330 9876536 + 7062771 df2 Chromosome Start End Strand Distance 0 chr1 1 1297 + 29071 1 chr1 1 1297 + 1247562 2 chr1 30367 33219 - 29071 3 chr1 30367 33219 - 1215640 4 chr1 1248858 1252096 + 169561 5 chr1 1248858 1252096 + 1215640 6 chr1 1421656 1428249 + 169561 7 chr1 1421656 1428249 + 1380817 8 chr1 2809065 2809560 + 1380817 9 chr1 2809065 2809560 + 1556970 10 chr1 8629188 8632609 + 1239722 11 chr1 8629188 8632609 + 5819629 12 chr1 9872330 9876536 + 1239722 13 chr1 9872330 9876536 + 7062771 Actual Chromosome Start End Strand Distance 0 chr1 1 1297 + 29071 1 chr1 1 1297 + 1247562 2 chr1 30367 33219 - 29071 3 chr1 30367 33219 - 1215640 4 chr1 1248858 1252096 + 169561 5 chr1 1248858 1252096 + 1215640 6 chr1 1421656 1428249 + 169561 7 chr1 1421656 1428249 + 1380817 8 chr1 2809065 2809560 + 1380817 9 chr1 2809065 2809560 + 1556970 10 chr1 8629188 8632609 + 1239722 11 chr1 8629188 8632609 + 5819629 12 chr1 9872330 9876536 + 1239722 13 chr1 9872330 9876536 + 7062771 Expected Chromosome Start End Strand Distance 0 chr1 1 1297 + 29071 1 chr1 1 1297 + 1247562 2 chr1 30367 33219 - 29071 3 chr1 30367 33219 - 1215640 4 chr1 1248858 1252096 + 169561 5 chr1 1248858 1252096 + 1215640 6 chr1 1421656 1428249 + 169561 7 chr1 1421656 1428249 + 1380817 8 chr1 2809065 2809560 + 1380817 9 chr1 2809065 2809560 + 1556970 10 chr1 8629188 8632609 + 1239722 11 chr1 8629188 8632609 + 5819629 12 chr1 9872330 9876536 + 1239722 13 chr1 9872330 9876536 + 7062771 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp19fsunr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19fsunr5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 941 - 2621516 1 chr1 2 942 - 2621515 2 chr1 30367 31307 - 30050 3 chr1 30367 31307 - 2591150 4 chr1 65537 66477 + 65220 5 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 8 chr1 2809065 2810005 + 186353 9 chr1 2809065 2810005 + 2808748 10 chr1 9872330 9872332 + 7249618 11 chr1 9872330 9872332 + 9872013 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 941 | a | 0 | ... | | chr1 | 30367 | 31307 | a | 0 | ... | | chr1 | 30367 | 31307 | a | 0 | ... | | chr1 | 2 | 942 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1 941 - 2621516 11 chr1 2 942 - 2621515 9 chr1 30367 31307 - 30050 10 chr1 30367 31307 - 2591150 2 chr1 65537 66477 + 65220 3 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 0 chr1 2809065 2810005 + 186353 1 chr1 2809065 2810005 + 2808748 4 chr1 9872330 9872332 + 7249618 5 chr1 9872330 9872332 + 9872013 df2 Chromosome Start End Strand Distance 0 chr1 1 941 - 2621516 1 chr1 2 942 - 2621515 2 chr1 30367 31307 - 30050 3 chr1 30367 31307 - 2591150 4 chr1 65537 66477 + 65220 5 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 8 chr1 2809065 2810005 + 186353 9 chr1 2809065 2810005 + 2808748 10 chr1 9872330 9872332 + 7249618 11 chr1 9872330 9872332 + 9872013 Actual Chromosome Start End Strand Distance 0 chr1 1 941 - 2621516 1 chr1 2 942 - 2621515 2 chr1 30367 31307 - 30050 3 chr1 30367 31307 - 2591150 4 chr1 65537 66477 + 65220 5 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 8 chr1 2809065 2810005 + 186353 9 chr1 2809065 2810005 + 2808748 10 chr1 9872330 9872332 + 7249618 11 chr1 9872330 9872332 + 9872013 Expected Chromosome Start End Strand Distance 0 chr1 1 941 - 2621516 1 chr1 2 942 - 2621515 2 chr1 30367 31307 - 30050 3 chr1 30367 31307 - 2591150 4 chr1 65537 66477 + 65220 5 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 8 chr1 2809065 2810005 + 186353 9 chr1 2809065 2810005 + 2808748 10 chr1 9872330 9872332 + 7249618 11 chr1 9872330 9872332 + 9872013 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpufjtvn24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufjtvn24/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | chr1 | 1421656 | 1421658 | a | 0 | ... | | chr1 | 30367 | 30368 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 4 chr1 65537 66477 - 65536 2 chr1 1421656 1421658 - 1421655 0 chr1 2809065 2810005 + 2809064 df2 Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 Actual Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Expected Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbk_mb4o_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbk_mb4o_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | chr1 | 1421656 | 1421658 | a | 0 | ... | | chr1 | 30367 | 30368 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 4 chr1 65537 66477 - 65536 2 chr1 1421656 1421658 - 1421655 0 chr1 2809065 2810005 + 2809064 df2 Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 Actual Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Expected Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdnoinqca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnoinqca/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | chr1 | 1421656 | 1421658 | a | 0 | ... | | chr1 | 30367 | 30368 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 4 chr1 65537 66477 - 65536 2 chr1 1421656 1421658 - 1421655 0 chr1 2809065 2810005 + 2809064 df2 Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 Actual Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Expected Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyfm_wsiy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfm_wsiy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqj8ct8e4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqj8ct8e4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 2 chr1 1359680 1366401 - 978662 3 chr1 2649568 2652676 - 304506 4 chr1 5519069 5520984 - 3174007 5 chr1 7636786 7639758 + 5291724 6 chr1 7726109 7733000 + 5381047 7 chr1 8786725 8794271 + 6441663 8 chr1 9450560 9457184 + 7105498 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7726109 | 7733000 | a | 0 | ... | | chr1 | 660331 | 662849 | a | 0 | ... | | chr1 | 8786725 | 8794271 | a | 0 | ... | | chr1 | 9450560 | 9457184 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 3203 | a | 0 | ... | | chr1 | 1359680 | 1366401 | a | 0 | ... | | chr1 | 5519069 | 5520984 | a | 0 | ... | | chr1 | 2649568 | 2652676 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 6 chr1 1359680 1366401 - 978662 8 chr1 2649568 2652676 - 304506 7 chr1 5519069 5520984 - 3174007 4 chr1 7636786 7639758 + 5291724 0 chr1 7726109 7733000 + 5381047 2 chr1 8786725 8794271 + 6441663 3 chr1 9450560 9457184 + 7105498 df2 Chromosome Start End Strand Distance 0 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 2 chr1 1359680 1366401 - 978662 3 chr1 2649568 2652676 - 304506 4 chr1 5519069 5520984 - 3174007 5 chr1 7636786 7639758 + 5291724 6 chr1 7726109 7733000 + 5381047 7 chr1 8786725 8794271 + 6441663 8 chr1 9450560 9457184 + 7105498 Actual Chromosome Start End Strand Distance 0 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 2 chr1 1359680 1366401 - 978662 3 chr1 2649568 2652676 - 304506 4 chr1 5519069 5520984 - 3174007 5 chr1 7636786 7639758 + 5291724 6 chr1 7726109 7733000 + 5381047 7 chr1 8786725 8794271 + 6441663 8 chr1 9450560 9457184 + 7105498 Expected Chromosome Start End Strand Distance 0 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 2 chr1 1359680 1366401 - 978662 3 chr1 2649568 2652676 - 304506 4 chr1 5519069 5520984 - 3174007 5 chr1 7636786 7639758 + 5291724 6 chr1 7726109 7733000 + 5381047 7 chr1 8786725 8794271 + 6441663 8 chr1 9450560 9457184 + 7105498 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcuyp1ruk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcuyp1ruk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8bzozm3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8bzozm3n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1o82jqot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o82jqot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj4feljz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4feljz6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf4lwhyn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4lwhyn8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp4aki9p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4aki9p4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp432yt1_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp432yt1_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpywjja3bd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpywjja3bd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjmao942r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjmao942r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 353014 + 277624 1 chr1 347873 353014 + 3257613 2 chr1 4453913 4463913 + 217294 3 chr1 4453913 4463913 + 836639 4 chr1 7382753 7384666 + 123943 5 chr1 7382753 7384666 + 2209390 6 chr1 8032598 8033237 + 773788 7 chr1 8032598 8033237 + 1560819 8 chr1 8696361 8697120 + 896936 9 chr1 8696361 8697120 + 1437551 14 chr22 7230165 7236079 - 100624 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8033237 | a | 0 | ... | | chr1 | 8032598 | 8033237 | a | 0 | ... | | chr1 | 8696361 | 8697120 | a | 0 | ... | | chr1 | 8696361 | 8697120 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7382753 | 7384666 | a | 0 | ... | | chr1 | 7382753 | 7384666 | a | 0 | ... | | chr1 | 4453913 | 4463913 | a | 0 | ... | | chr1 | 4453913 | 4463913 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 347873 353014 + 277624 5 chr1 347873 353014 + 3257613 8 chr1 4453913 4463913 + 217294 9 chr1 4453913 4463913 + 836639 10 chr22 7230165 7236079 - 100624 6 chr1 7382753 7384666 + 123943 7 chr1 7382753 7384666 + 2209390 0 chr1 8032598 8033237 + 773788 1 chr1 8032598 8033237 + 1560819 2 chr1 8696361 8697120 + 896936 3 chr1 8696361 8697120 + 1437551 df2 Chromosome Start End Strand Distance 0 chr1 347873 353014 + 277624 1 chr1 347873 353014 + 3257613 2 chr1 4453913 4463913 + 217294 3 chr1 4453913 4463913 + 836639 14 chr22 7230165 7236079 - 100624 4 chr1 7382753 7384666 + 123943 5 chr1 7382753 7384666 + 2209390 6 chr1 8032598 8033237 + 773788 7 chr1 8032598 8033237 + 1560819 8 chr1 8696361 8697120 + 896936 9 chr1 8696361 8697120 + 1437551 Actual Chromosome Start End Strand Distance 0 chr1 347873 353014 + 277624 1 chr1 347873 353014 + 3257613 2 chr1 4453913 4463913 + 217294 3 chr1 4453913 4463913 + 836639 4 chr1 7382753 7384666 + 123943 5 chr1 7382753 7384666 + 2209390 6 chr1 8032598 8033237 + 773788 7 chr1 8032598 8033237 + 1560819 8 chr1 8696361 8697120 + 896936 9 chr1 8696361 8697120 + 1437551 10 chr22 7230165 7236079 - 100624 Expected Chromosome Start End Strand Distance 0 chr1 347873 353014 + 277624 1 chr1 347873 353014 + 3257613 2 chr1 4453913 4463913 + 217294 3 chr1 4453913 4463913 + 836639 4 chr1 7382753 7384666 + 123943 5 chr1 7382753 7384666 + 2209390 6 chr1 8032598 8033237 + 773788 7 chr1 8032598 8033237 + 1560819 8 chr1 8696361 8697120 + 896936 9 chr1 8696361 8697120 + 1437551 10 chr22 7230165 7236079 - 100624 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzqw2n_g6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqw2n_g6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282335 4 chr1 4453913 4453920 - 4388375 3 chr1 7382753 7382998 - 7317215 0 chr1 8032598 8032599 - 7967060 1 chr1 8696361 8696362 - 8630823 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw1q4ob8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1q4ob8k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 8 chr2 2080758 2087840 - 2014965 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | | chr2 | 2080758 | 2087840 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282335 5 chr2 2080758 2087840 - 2014965 4 chr1 4453913 4453920 - 4388375 3 chr1 7382753 7382998 - 7317215 0 chr1 8032598 8032599 - 7967060 1 chr1 8696361 8696362 - 8630823 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 8 chr2 2080758 2087840 - 2014965 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplbcsbtgb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbcsbtgb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 8 chr2 2080758 2087840 - 2014965 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | | chr2 | 2080758 | 2087840 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282335 5 chr2 2080758 2087840 - 2014965 4 chr1 4453913 4453920 - 4388375 3 chr1 7382753 7382998 - 7317215 0 chr1 8032598 8032599 - 7967060 1 chr1 8696361 8696362 - 8630823 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 8 chr2 2080758 2087840 - 2014965 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp1q8n2fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1q8n2fa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 7 chr2 2080758 2087840 - 2014965 8 chr2 6821396 6825749 - 6755603 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | | chr2 | 6821396 | 6825749 | a | 0 | ... | | chr2 | 2080758 | 2087840 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282335 6 chr2 2080758 2087840 - 2014965 4 chr1 4453913 4453920 - 4388375 5 chr2 6821396 6825749 - 6755603 3 chr1 7382753 7382998 - 7317215 0 chr1 8032598 8032599 - 7967060 1 chr1 8696361 8696362 - 8630823 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 7 chr2 2080758 2087840 - 2014965 1 chr1 4453913 4453920 - 4388375 8 chr2 6821396 6825749 - 6755603 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 6 chr2 6821396 6825749 - 6755603 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 6 chr2 6821396 6825749 - 6755603 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuktpqhp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuktpqhp6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282328 1 chr1 4453913 4453920 - 4388368 2 chr1 7382753 7382998 - 7317208 3 chr1 8032598 8032599 - 7967053 4 chr1 8696361 8696362 - 8630816 7 chr2 2080758 2087840 - 2080754 8 chr2 6821396 6825749 - 6821392 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | | chr2 | 6821396 | 6825749 | a | 0 | ... | | chr2 | 2080758 | 2087840 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282328 6 chr2 2080758 2087840 - 2080754 4 chr1 4453913 4453920 - 4388368 5 chr2 6821396 6825749 - 6821392 3 chr1 7382753 7382998 - 7317208 0 chr1 8032598 8032599 - 7967053 1 chr1 8696361 8696362 - 8630816 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282328 7 chr2 2080758 2087840 - 2080754 1 chr1 4453913 4453920 - 4388368 8 chr2 6821396 6825749 - 6821392 2 chr1 7382753 7382998 - 7317208 3 chr1 8032598 8032599 - 7967053 4 chr1 8696361 8696362 - 8630816 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282328 1 chr1 4453913 4453920 - 4388368 2 chr1 7382753 7382998 - 7317208 3 chr1 8032598 8032599 - 7967053 4 chr1 8696361 8696362 - 8630816 5 chr2 2080758 2087840 - 2080754 6 chr2 6821396 6825749 - 6821392 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282328 1 chr1 4453913 4453920 - 4388368 2 chr1 7382753 7382998 - 7317208 3 chr1 8032598 8032599 - 7967053 4 chr1 8696361 8696362 - 8630816 5 chr2 2080758 2087840 - 2080754 6 chr2 6821396 6825749 - 6821392 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf_798kt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_798kt4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 1 chr1 9 1368 - 64170 2 chr1 9 8202 - 57336 3 chr1 65537 70914 - 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9 | 10 | a | 0 | ... | | chr1 | 65537 | 70914 | a | 0 | ... | | chr1 | 9 | 1368 | a | 0 | ... | | chr1 | 9 | 8202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 2 chr1 9 1368 - 64170 3 chr1 9 8202 - 57336 1 chr1 65537 70914 - 65280 df2 Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 1 chr1 9 1368 - 64170 2 chr1 9 8202 - 57336 3 chr1 65537 70914 - 65280 Actual Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 1 chr1 9 1368 - 64170 2 chr1 9 8202 - 57336 3 chr1 65537 70914 - 65280 Expected Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 1 chr1 9 1368 - 64170 2 chr1 9 8202 - 57336 3 chr1 65537 70914 - 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq_vgsdck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_vgsdck/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 858392 861950 - 851397 3 chr1 858392 861950 - 2919506 0 chr1 7364263 7372460 + 1955678 1 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0szlemom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0szlemom/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 858392 861950 - 851397 3 chr1 858392 861950 - 2919506 0 chr1 7364263 7372460 + 1955678 1 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo3humml5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo3humml5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 792855 1 chr1 858392 861950 - 858383 2 chr1 7364263 7372460 + 7298726 3 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 858392 861950 - 792855 3 chr1 858392 861950 - 858383 0 chr1 7364263 7372460 + 7298726 1 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 792855 1 chr1 858392 861950 - 858383 2 chr1 7364263 7372460 + 7298726 3 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 792855 1 chr1 858392 861950 - 858383 2 chr1 7364263 7372460 + 7298726 3 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 792855 1 chr1 858392 861950 - 858383 2 chr1 7364263 7372460 + 7298726 3 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgqq87cey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqq87cey/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 6502314 1 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 858392 861950 - 6502314 0 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 6502314 1 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 6502314 1 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 6502314 1 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi37zx17t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi37zx17t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 1 chr1 7364263 7372460 - 7363947 2 chr1 7364263 7373652 - 7363947 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | | chr1 | 7364263 | 7372460 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 2 chr1 7364263 7372460 - 7363947 1 chr1 7364263 7373652 - 7363947 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 1 chr1 7364263 7372460 - 7363947 2 chr1 7364263 7373652 - 7363947 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 1 chr1 7364263 7372460 - 7363947 2 chr1 7364263 7373652 - 7363947 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 1 chr1 7364263 7372460 - 7363947 2 chr1 7364263 7373652 - 7363947 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplait83vw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplait83vw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr10 9925858 9926922 - 9925542 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr10 | 9925858 | 9926922 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9925542 df2 Chromosome Start End Strand Distance 3 chr10 9925858 9926922 - 9925542 Actual Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9925542 Expected Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9925542 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpabskdmn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabskdmn6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr10 9925858 9926922 - 9919794 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr10 | 9925858 | 9926922 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9919794 df2 Chromosome Start End Strand Distance 3 chr10 9925858 9926922 - 9919794 Actual Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9919794 Expected Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9919794 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5w6vitwe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5w6vitwe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1156855 1162997 - 1099643 9 chr1 1156855 1162997 - 1716765 6 chr1 3548283 3548906 + 663688 7 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 0 chr1 6767787 6777786 + 1367537 1 chr1 6767787 6777786 + 2111800 2 chr1 6886548 6887717 + 1257606 3 chr1 6886548 6887717 + 2001869 df2 Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Actual Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Expected Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvrrfy5wz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrrfy5wz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1156855 1162997 - 1099643 9 chr1 1156855 1162997 - 1716765 6 chr1 3548283 3548906 + 663688 7 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 0 chr1 6767787 6777786 + 1367537 1 chr1 6767787 6777786 + 2111800 2 chr1 6886548 6887717 + 1257606 3 chr1 6886548 6887717 + 2001869 df2 Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Actual Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Expected Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpboqdlqmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpboqdlqmr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1091062 1 chr1 1156855 1162997 - 1156595 2 chr1 3548283 3548906 + 3482490 3 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 6 chr1 6767787 6777786 + 6701994 7 chr1 6767787 6777786 + 6767527 8 chr1 6886548 6887717 + 6820755 9 chr1 6886548 6887717 + 6886288 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1156855 1162997 - 1091062 9 chr1 1156855 1162997 - 1156595 6 chr1 3548283 3548906 + 3482490 7 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 0 chr1 6767787 6777786 + 6701994 1 chr1 6767787 6777786 + 6767527 2 chr1 6886548 6887717 + 6820755 3 chr1 6886548 6887717 + 6886288 df2 Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1091062 1 chr1 1156855 1162997 - 1156595 2 chr1 3548283 3548906 + 3482490 3 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 6 chr1 6767787 6777786 + 6701994 7 chr1 6767787 6777786 + 6767527 8 chr1 6886548 6887717 + 6820755 9 chr1 6886548 6887717 + 6886288 Actual Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1091062 1 chr1 1156855 1162997 - 1156595 2 chr1 3548283 3548906 + 3482490 3 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 6 chr1 6767787 6777786 + 6701994 7 chr1 6767787 6777786 + 6767527 8 chr1 6886548 6887717 + 6820755 9 chr1 6886548 6887717 + 6886288 Expected Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1091062 1 chr1 1156855 1162997 - 1156595 2 chr1 3548283 3548906 + 3482490 3 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 6 chr1 6767787 6777786 + 6701994 7 chr1 6767787 6777786 + 6767527 8 chr1 6886548 6887717 + 6820755 9 chr1 6886548 6887717 + 6886288 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpue7crmba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpue7crmba/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 3 chr2 4 6 - 74 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 9 | a | 0 | ... | | chr2 | 4 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 2 chr2 4 6 - 74 1 chr1 4 9 - 65529 df2 Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 3 chr2 4 6 - 74 1 chr1 4 9 - 65529 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 6 - 74 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 6 - 74 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpofdqf06w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofdqf06w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 5 - 75 3 chr2 4 6 - 74 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 9 | a | 0 | ... | | chr2 | 4 | 5 | a | 0 | ... | | chr2 | 4 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr2 4 5 - 75 0 chr1 4 5 - 65533 3 chr2 4 6 - 74 1 chr1 4 9 - 65529 df2 Chromosome Start End Strand Distance 2 chr2 4 5 - 75 0 chr1 4 5 - 65533 3 chr2 4 6 - 74 1 chr1 4 9 - 65529 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 5 - 75 3 chr2 4 6 - 74 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 5 - 75 3 chr2 4 6 - 74 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48siqggx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48siqggx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5mgfr8kx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mgfr8kx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjclx042r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjclx042r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5918092 5918311 - 21998 1 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 4 chr1 8966121 8966122 - 3070027 5 chr1 8966121 8966122 - 3093082 6 chr1 9519744 9526725 + 3623650 7 chr1 9519744 9526725 + 3646705 9 chr14 4273233 4280094 + 976476 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9519744 | 9526725 | a | 0 | ... | | chr1 | 9519744 | 9526725 | a | 0 | ... | | chr1 | 8340730 | 8343567 | a | 0 | ... | | chr1 | 8340730 | 8343567 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5918092 | 5918311 | a | 0 | ... | | chr1 | 5918092 | 5918311 | a | 0 | ... | | chr1 | 8966121 | 8966122 | a | 0 | ... | | chr1 | 8966121 | 8966122 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr14 4273233 4280094 + 976476 4 chr1 5918092 5918311 - 21998 5 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 6 chr1 8966121 8966122 - 3070027 7 chr1 8966121 8966122 - 3093082 0 chr1 9519744 9526725 + 3623650 1 chr1 9519744 9526725 + 3646705 df2 Chromosome Start End Strand Distance 9 chr14 4273233 4280094 + 976476 0 chr1 5918092 5918311 - 21998 1 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 4 chr1 8966121 8966122 - 3070027 5 chr1 8966121 8966122 - 3093082 6 chr1 9519744 9526725 + 3623650 7 chr1 9519744 9526725 + 3646705 Actual Chromosome Start End Strand Distance 0 chr1 5918092 5918311 - 21998 1 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 4 chr1 8966121 8966122 - 3070027 5 chr1 8966121 8966122 - 3093082 6 chr1 9519744 9526725 + 3623650 7 chr1 9519744 9526725 + 3646705 8 chr14 4273233 4280094 + 976476 Expected Chromosome Start End Strand Distance 0 chr1 5918092 5918311 - 21998 1 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 4 chr1 8966121 8966122 - 3070027 5 chr1 8966121 8966122 - 3093082 6 chr1 9519744 9526725 + 3623650 7 chr1 9519744 9526725 + 3646705 8 chr14 4273233 4280094 + 976476 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx18qc56g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx18qc56g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4420 | a | 0 | ... | | chr12 | 6 | 263 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 df2 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Expected Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2pz6i6j_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2pz6i6j_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4420 | a | 0 | ... | | chr12 | 6 | 263 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 df2 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Expected Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8po1tmtn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8po1tmtn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4420 | a | 0 | ... | | chr12 | 6 | 263 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 df2 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Expected Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj4y65njs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4y65njs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg_1ffd_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_1ffd_z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 258 + 65280 2 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 65536 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 258 + 65280 2 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 258 + 65280 2 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 258 + 65280 2 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsrh6qa5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsrh6qa5l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 6 chr8 680946 685979 + 658932 7 chrM 10000000 10003046 + 9477394 8 chrM 10000000 10009242 - 9477394 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10010000 | a | 0 | ... | | chr1 | 10000000 | 10010000 | a | 0 | ... | | chr8 | 680946 | 685979 | a | 0 | ... | | chrM | 10000000 | 10003046 | a | 0 | ... | | chrM | 10000000 | 10009242 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr8 680946 685979 + 658932 3 chrM 10000000 10003046 + 9477394 4 chrM 10000000 10009242 - 9477394 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 df2 Chromosome Start End Strand Distance 6 chr8 680946 685979 + 658932 7 chrM 10000000 10003046 + 9477394 8 chrM 10000000 10009242 - 9477394 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 Actual Chromosome Start End Strand Distance 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 2 chr8 680946 685979 + 658932 3 chrM 10000000 10003046 + 9477394 4 chrM 10000000 10009242 - 9477394 Expected Chromosome Start End Strand Distance 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 2 chr8 680946 685979 + 658932 3 chrM 10000000 10003046 + 9477394 4 chrM 10000000 10009242 - 9477394 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe9ijo35d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9ijo35d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpma2n9aqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma2n9aqq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr18 6284987 6287624 + 6284978 3 chr2 10000000 10002433 - 9997564 4 chr2 10000000 10002433 - 9999979 5 chr7 10000000 10000712 - 9999915 7 chrM 10000000 10003046 + 9997562 8 chrM 10000000 10009242 - 9997562 9 chrY 3329340 3336894 + 3329211 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 10000000 | 10002433 | a | 0 | ... | | chr2 | 10000000 | 10002433 | a | 0 | ... | | chr7 | 10000000 | 10000712 | a | 0 | ... | | chr18 | 6284987 | 6287624 | a | 0 | ... | | chrM | 10000000 | 10003046 | a | 0 | ... | | chrM | 10000000 | 10009242 | a | 0 | ... | | chrY | 3329340 | 3336894 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chrY 3329340 3336894 + 3329211 3 chr18 6284987 6287624 + 6284978 2 chr7 10000000 10000712 - 9999915 0 chr2 10000000 10002433 - 9997564 1 chr2 10000000 10002433 - 9999979 4 chrM 10000000 10003046 + 9997562 5 chrM 10000000 10009242 - 9997562 df2 Chromosome Start End Strand Distance 9 chrY 3329340 3336894 + 3329211 2 chr18 6284987 6287624 + 6284978 5 chr7 10000000 10000712 - 9999915 3 chr2 10000000 10002433 - 9997564 4 chr2 10000000 10002433 - 9999979 7 chrM 10000000 10003046 + 9997562 8 chrM 10000000 10009242 - 9997562 Actual Chromosome Start End Strand Distance 0 chr18 6284987 6287624 + 6284978 1 chr2 10000000 10002433 - 9997564 2 chr2 10000000 10002433 - 9999979 3 chr7 10000000 10000712 - 9999915 4 chrM 10000000 10003046 + 9997562 5 chrM 10000000 10009242 - 9997562 6 chrY 3329340 3336894 + 3329211 Expected Chromosome Start End Strand Distance 0 chr18 6284987 6287624 + 6284978 1 chr2 10000000 10002433 - 9997564 2 chr2 10000000 10002433 - 9999979 3 chr7 10000000 10000712 - 9999915 4 chrM 10000000 10003046 + 9997562 5 chrM 10000000 10009242 - 9997562 6 chrY 3329340 3336894 + 3329211 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5js1sztf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5js1sztf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 4 | 2437 | a | 0 | ... | | chr2 | 6 | 13 | a | 0 | ... | | chr2 | 7 | 12 | a | 0 | ... | | chr2 | 15 | 22 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 df2 Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 Actual Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Expected Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5pp6jl9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pp6jl9v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 4 | 2437 | a | 0 | ... | | chr2 | 6 | 13 | a | 0 | ... | | chr2 | 7 | 12 | a | 0 | ... | | chr2 | 15 | 22 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 df2 Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 Actual Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Expected Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp22c0yq9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp22c0yq9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 4 | 2437 | a | 0 | ... | | chr2 | 6 | 13 | a | 0 | ... | | chr2 | 7 | 12 | a | 0 | ... | | chr2 | 15 | 22 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 df2 Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 Actual Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Expected Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_s3zbdsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_s3zbdsu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 4 | 2437 | a | 0 | ... | | chr2 | 6 | 13 | a | 0 | ... | | chr2 | 7 | 12 | a | 0 | ... | | chr2 | 15 | 22 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 df2 Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 Actual Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Expected Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt2rnz_jg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2rnz_jg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpskpa4m6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskpa4m6e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiwh8g_jm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiwh8g_jm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6eo033n0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6eo033n0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr12 | 9167475 | 9171432 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 df2 Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 Actual Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 Expected Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmgr9ij2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmgr9ij2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr12 | 9167475 | 9171432 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 df2 Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 Actual Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 Expected Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl0rdtcws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0rdtcws/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr12 | 11 | 3968 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 df2 Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Actual Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Expected Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxzxycjv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxzxycjv6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr12 | 11 | 3968 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 df2 Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Actual Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Expected Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphk503crf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphk503crf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 3650420 | 3652943 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 4 chr1 2841009 2849202 - 1333010 3 chr1 3650420 3652943 - 529269 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5hj7uv2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hj7uv2t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 3650420 | 3652943 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 4 chr1 2841009 2849202 - 1333010 3 chr1 3650420 3652943 - 529269 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9eo5e3og/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9eo5e3og/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 3 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpodfnopen/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodfnopen/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 3 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzmk6l5_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmk6l5_9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 3 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps0l4fcrt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0l4fcrt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2426064 - 2425804 1 chr1 2841009 2841012 - 2840752 2 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3753195 | 3761216 | a | 0 | ... | | chr1 | 2426061 | 2426064 | a | 0 | ... | | chr1 | 2841009 | 2841012 | a | 0 | ... | | chr1 | 5646943 | 5646946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2426061 2426064 - 2425804 2 chr1 2841009 2841012 - 2840752 0 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2426064 - 2425804 1 chr1 2841009 2841012 - 2840752 2 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2426064 - 2425804 1 chr1 2841009 2841012 - 2840752 2 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2426064 - 2425804 1 chr1 2841009 2841012 - 2840752 2 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmuy8xcyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmuy8xcyl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 6016 | a | 0 | ... | | chr1 | 2 | 6016 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 4 chr1 2071439 2074140 - 432071 5 chr1 2071439 2074140 - 708902 2 chr1 6824194 6832392 + 237914 3 chr1 6824194 6832392 + 2363578 8 chr1 6824194 6832946 - 237360 9 chr1 6824194 6832946 - 2363578 6 chr1 8134000 8141150 - 1055989 7 chr1 8134000 8141150 - 3673384 df2 Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Actual Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Expected Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaktfu6i5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaktfu6i5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9003 | a | 0 | ... | | chr1 | 2 | 9003 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 4 chr1 2071439 2074140 - 432071 5 chr1 2071439 2074140 - 708902 2 chr1 6824194 6832392 + 237914 3 chr1 6824194 6832392 + 2363578 8 chr1 6824194 6832946 - 237360 9 chr1 6824194 6832946 - 2363578 6 chr1 8134000 8141150 - 1055989 7 chr1 8134000 8141150 - 3673384 df2 Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Actual Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Expected Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuehurhwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuehurhwm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 1 chr1 2071439 2074140 - 2005900 2 chr1 2071439 2074140 - 2071174 3 chr1 6824194 6832392 + 6758655 4 chr1 6824194 6832392 + 6823929 5 chr1 6824194 6832946 - 6758655 6 chr1 6824194 6832946 - 6823929 7 chr1 8134000 8141150 - 8068461 8 chr1 8134000 8141150 - 8133735 10 chr2 6824194 6826141 - 6758655 11 chr2 6824194 6826141 - 6824193 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9003 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 2071439 | 2074140 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 3 chr1 2071439 2074140 - 2005900 4 chr1 2071439 2074140 - 2071174 9 chr2 6824194 6826141 - 6758655 10 chr2 6824194 6826141 - 6824193 1 chr1 6824194 6832392 + 6758655 2 chr1 6824194 6832392 + 6823929 7 chr1 6824194 6832946 - 6758655 8 chr1 6824194 6832946 - 6823929 5 chr1 8134000 8141150 - 8068461 6 chr1 8134000 8141150 - 8133735 df2 Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 1 chr1 2071439 2074140 - 2005900 2 chr1 2071439 2074140 - 2071174 10 chr2 6824194 6826141 - 6758655 11 chr2 6824194 6826141 - 6824193 3 chr1 6824194 6832392 + 6758655 4 chr1 6824194 6832392 + 6823929 5 chr1 6824194 6832946 - 6758655 6 chr1 6824194 6832946 - 6823929 7 chr1 8134000 8141150 - 8068461 8 chr1 8134000 8141150 - 8133735 Actual Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 1 chr1 2071439 2074140 - 2005900 2 chr1 2071439 2074140 - 2071174 3 chr1 6824194 6832392 + 6758655 4 chr1 6824194 6832392 + 6823929 5 chr1 6824194 6832946 - 6758655 6 chr1 6824194 6832946 - 6823929 7 chr1 8134000 8141150 - 8068461 8 chr1 8134000 8141150 - 8133735 9 chr2 6824194 6826141 - 6758655 10 chr2 6824194 6826141 - 6824193 Expected Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 1 chr1 2071439 2074140 - 2005900 2 chr1 2071439 2074140 - 2071174 3 chr1 6824194 6832392 + 6758655 4 chr1 6824194 6832392 + 6823929 5 chr1 6824194 6832946 - 6758655 6 chr1 6824194 6832946 - 6823929 7 chr1 8134000 8141150 - 8068461 8 chr1 8134000 8141150 - 8133735 9 chr2 6824194 6826141 - 6758655 10 chr2 6824194 6826141 - 6824193 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpud0qt429/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpud0qt429/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 1 chr1 2071439 2074140 - 2071432 2 chr1 2071439 2074140 - 2071436 3 chr1 6824194 6832392 + 6824187 4 chr1 6824194 6832392 + 6824191 5 chr1 6824194 6832946 - 6824187 6 chr1 6824194 6832946 - 6824191 7 chr1 8134000 8141150 - 8133993 8 chr1 8134000 8141150 - 8133997 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9003 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 2071439 | 2074140 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 3 chr1 2071439 2074140 - 2071432 4 chr1 2071439 2074140 - 2071436 1 chr1 6824194 6832392 + 6824187 2 chr1 6824194 6832392 + 6824191 7 chr1 6824194 6832946 - 6824187 8 chr1 6824194 6832946 - 6824191 5 chr1 8134000 8141150 - 8133993 6 chr1 8134000 8141150 - 8133997 df2 Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 1 chr1 2071439 2074140 - 2071432 2 chr1 2071439 2074140 - 2071436 3 chr1 6824194 6832392 + 6824187 4 chr1 6824194 6832392 + 6824191 5 chr1 6824194 6832946 - 6824187 6 chr1 6824194 6832946 - 6824191 7 chr1 8134000 8141150 - 8133993 8 chr1 8134000 8141150 - 8133997 Actual Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 1 chr1 2071439 2074140 - 2071432 2 chr1 2071439 2074140 - 2071436 3 chr1 6824194 6832392 + 6824187 4 chr1 6824194 6832392 + 6824191 5 chr1 6824194 6832946 - 6824187 6 chr1 6824194 6832946 - 6824191 7 chr1 8134000 8141150 - 8133993 8 chr1 8134000 8141150 - 8133997 Expected Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 1 chr1 2071439 2074140 - 2071432 2 chr1 2071439 2074140 - 2071436 3 chr1 6824194 6832392 + 6824187 4 chr1 6824194 6832392 + 6824191 5 chr1 6824194 6832946 - 6824187 6 chr1 6824194 6832946 - 6824191 7 chr1 8134000 8141150 - 8133993 8 chr1 8134000 8141150 - 8133997 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpudk0uz62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudk0uz62/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 8 chr1 3 4 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 0 chr1 3 4 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 8 chr1 3 4 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 3 4 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 3 4 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqscl3i6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqscl3i6e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqnnd552/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqnnd552/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 8 chr1 3 4 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 0 chr1 3 4 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 8 chr1 3 4 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 3 4 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 3 4 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpse1zy4xs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpse1zy4xs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2393623 2399974 - 310353 1 chr1 2393623 2399974 - 356532 2 chr1 6863831 6865563 + 1660709 3 chr1 6863831 6865563 + 4098447 4 chr14 1132263 1132264 - 4765783 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6863831 | 6865563 | a | 0 | ... | | chr1 | 6863831 | 6865563 | a | 0 | ... | | chr1 | 2393623 | 2399974 | a | 0 | ... | | chr1 | 2393623 | 2399974 | a | 0 | ... | | chr14 | 1132263 | 1132264 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr14 1132263 1132264 - 4765783 2 chr1 2393623 2399974 - 310353 3 chr1 2393623 2399974 - 356532 0 chr1 6863831 6865563 + 1660709 1 chr1 6863831 6865563 + 4098447 df2 Chromosome Start End Strand Distance 4 chr14 1132263 1132264 - 4765783 0 chr1 2393623 2399974 - 310353 1 chr1 2393623 2399974 - 356532 2 chr1 6863831 6865563 + 1660709 3 chr1 6863831 6865563 + 4098447 Actual Chromosome Start End Strand Distance 0 chr1 2393623 2399974 - 310353 1 chr1 2393623 2399974 - 356532 2 chr1 6863831 6865563 + 1660709 3 chr1 6863831 6865563 + 4098447 4 chr14 1132263 1132264 - 4765783 Expected Chromosome Start End Strand Distance 0 chr1 2393623 2399974 - 310353 1 chr1 2393623 2399974 - 356532 2 chr1 6863831 6865563 + 1660709 3 chr1 6863831 6865563 + 4098447 4 chr14 1132263 1132264 - 4765783 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmr8kobvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmr8kobvi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 5814626 2 chr1 2756505 2765385 - 44860 3 chr1 2756505 2765385 - 5760887 4 chr1 8526271 8532264 - 5760887 5 chr1 8526271 8532264 - 5814626 9 chr7 1003501 1007391 + 7602428 10 chr7 1003501 1007391 + 7945813 11 chr7 8609818 8618678 - 334526 12 chr7 8609818 8618678 - 7602428 13 chr7 8953203 8953482 - 334526 14 chr7 8953203 8953482 - 7945813 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr7 | 8609818 | 8618678 | a | 0 | ... | | chr7 | 8609818 | 8618678 | a | 0 | ... | | chr7 | 8953203 | 8953482 | a | 0 | ... | | chr7 | 8953203 | 8953482 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr7 1003501 1007391 + 7602428 7 chr7 1003501 1007391 + 7945813 4 chr1 2710326 2711646 - 44860 5 chr1 2710326 2711646 - 5814626 0 chr1 2756505 2765385 - 44860 1 chr1 2756505 2765385 - 5760887 2 chr1 8526271 8532264 - 5760887 3 chr1 8526271 8532264 - 5814626 8 chr7 8609818 8618678 - 334526 9 chr7 8609818 8618678 - 7602428 10 chr7 8953203 8953482 - 334526 11 chr7 8953203 8953482 - 7945813 df2 Chromosome Start End Strand Distance 9 chr7 1003501 1007391 + 7602428 10 chr7 1003501 1007391 + 7945813 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 5814626 2 chr1 2756505 2765385 - 44860 3 chr1 2756505 2765385 - 5760887 4 chr1 8526271 8532264 - 5760887 5 chr1 8526271 8532264 - 5814626 11 chr7 8609818 8618678 - 334526 12 chr7 8609818 8618678 - 7602428 13 chr7 8953203 8953482 - 334526 14 chr7 8953203 8953482 - 7945813 Actual Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 5814626 2 chr1 2756505 2765385 - 44860 3 chr1 2756505 2765385 - 5760887 4 chr1 8526271 8532264 - 5760887 5 chr1 8526271 8532264 - 5814626 6 chr7 1003501 1007391 + 7602428 7 chr7 1003501 1007391 + 7945813 8 chr7 8609818 8618678 - 334526 9 chr7 8609818 8618678 - 7602428 10 chr7 8953203 8953482 - 334526 11 chr7 8953203 8953482 - 7945813 Expected Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 5814626 2 chr1 2756505 2765385 - 44860 3 chr1 2756505 2765385 - 5760887 4 chr1 8526271 8532264 - 5760887 5 chr1 8526271 8532264 - 5814626 6 chr7 1003501 1007391 + 7602428 7 chr7 1003501 1007391 + 7945813 8 chr7 8609818 8618678 - 334526 9 chr7 8609818 8618678 - 7602428 10 chr7 8953203 8953482 - 334526 11 chr7 8953203 8953482 - 7945813 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9w8_7ak1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9w8_7ak1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5767561 7 chr14 5898046 5902152 - 3141533 8 chr2 9027365 9030522 - 6268365 9 chr2 9027365 9030522 - 9027309 13 chrM 1881625 1883952 - 872554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chr14 | 5898046 | 5902152 | a | 0 | ... | | chrM | 1881625 | 1883952 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 9 chrM 1881625 1883952 - 872554 4 chr1 2710326 2711646 - 44860 5 chr1 2710326 2711646 - 2642143 0 chr1 2756505 2765385 - 2688322 1 chr1 2756505 2765385 - 2690968 8 chr14 5898046 5902152 - 3141533 2 chr1 8526271 8532264 - 5763798 3 chr1 8526271 8532264 - 5767561 6 chr2 9027365 9030522 - 6268365 7 chr2 9027365 9030522 - 9027309 df2 Chromosome Start End Strand Distance 13 chrM 1881625 1883952 - 872554 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 7 chr14 5898046 5902152 - 3141533 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5767561 8 chr2 9027365 9030522 - 6268365 9 chr2 9027365 9030522 - 9027309 Actual Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5767561 6 chr14 5898046 5902152 - 3141533 7 chr2 9027365 9030522 - 6268365 8 chr2 9027365 9030522 - 9027309 9 chrM 1881625 1883952 - 872554 Expected Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5767561 6 chr14 5898046 5902152 - 3141533 7 chr2 9027365 9030522 - 6268365 8 chr2 9027365 9030522 - 9027309 9 chrM 1881625 1883952 - 872554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1rra1yfy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rra1yfy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5769229 7 chr14 5898046 5902152 - 3139336 8 chr2 9027365 9030522 - 6268365 9 chr2 9027365 9030522 - 9027309 13 chrM 1881625 1883952 - 872554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chr14 | 5898046 | 5902152 | a | 0 | ... | | chrM | 1881625 | 1883952 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 9 chrM 1881625 1883952 - 872554 4 chr1 2710326 2711646 - 44860 5 chr1 2710326 2711646 - 2642143 0 chr1 2756505 2765385 - 2688322 1 chr1 2756505 2765385 - 2690968 8 chr14 5898046 5902152 - 3139336 2 chr1 8526271 8532264 - 5763798 3 chr1 8526271 8532264 - 5769229 6 chr2 9027365 9030522 - 6268365 7 chr2 9027365 9030522 - 9027309 df2 Chromosome Start End Strand Distance 13 chrM 1881625 1883952 - 872554 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 7 chr14 5898046 5902152 - 3139336 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5769229 8 chr2 9027365 9030522 - 6268365 9 chr2 9027365 9030522 - 9027309 Actual Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5769229 6 chr14 5898046 5902152 - 3139336 7 chr2 9027365 9030522 - 6268365 8 chr2 9027365 9030522 - 9027309 9 chrM 1881625 1883952 - 872554 Expected Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5769229 6 chr14 5898046 5902152 - 3139336 7 chr2 9027365 9030522 - 6268365 8 chr2 9027365 9030522 - 9027309 9 chrM 1881625 1883952 - 872554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvsqbc2qb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsqbc2qb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 2703649 1 chr1 2710326 2711646 - 2704176 2 chr1 2756505 2765385 + 2749828 3 chr1 2756505 2765385 + 2750355 4 chr1 8526271 8532264 - 8519594 5 chr1 8526271 8532264 - 8520121 8 chr2 9027365 9030522 - 9024864 12 chrM 1881625 1883952 - 1874274 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 2710326 | 2711646 | a | 0 | ... | | chr1 | 2710326 | 2711646 | a | 0 | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chrM | 1881625 | 1883952 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chrM 1881625 1883952 - 1874274 4 chr1 2710326 2711646 - 2703649 5 chr1 2710326 2711646 - 2704176 0 chr1 2756505 2765385 + 2749828 1 chr1 2756505 2765385 + 2750355 2 chr1 8526271 8532264 - 8519594 3 chr1 8526271 8532264 - 8520121 6 chr2 9027365 9030522 - 9024864 df2 Chromosome Start End Strand Distance 12 chrM 1881625 1883952 - 1874274 0 chr1 2710326 2711646 - 2703649 1 chr1 2710326 2711646 - 2704176 2 chr1 2756505 2765385 + 2749828 3 chr1 2756505 2765385 + 2750355 4 chr1 8526271 8532264 - 8519594 5 chr1 8526271 8532264 - 8520121 8 chr2 9027365 9030522 - 9024864 Actual Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 2703649 1 chr1 2710326 2711646 - 2704176 2 chr1 2756505 2765385 + 2749828 3 chr1 2756505 2765385 + 2750355 4 chr1 8526271 8532264 - 8519594 5 chr1 8526271 8532264 - 8520121 6 chr2 9027365 9030522 - 9024864 7 chrM 1881625 1883952 - 1874274 Expected Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 2703649 1 chr1 2710326 2711646 - 2704176 2 chr1 2756505 2765385 + 2749828 3 chr1 2756505 2765385 + 2750355 4 chr1 8526271 8532264 - 8519594 5 chr1 8526271 8532264 - 8520121 6 chr2 9027365 9030522 - 9024864 7 chrM 1881625 1883952 - 1874274 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8dxxzpyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dxxzpyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 65537 71530 - 58860 2 chr1 65537 71530 - 59387 3 chr1 65537 74417 + 58860 4 chr1 65537 74417 + 59387 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 74417 | a | 0 | ... | | chr1 | 65537 | 74417 | a | 0 | ... | | chr1 | 65537 | 71530 | a | 0 | ... | | chr1 | 65537 | 71530 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 65537 71530 - 58860 3 chr1 65537 71530 - 59387 0 chr1 65537 74417 + 58860 1 chr1 65537 74417 + 59387 df2 Chromosome Start End Strand Distance 1 chr1 65537 71530 - 58860 2 chr1 65537 71530 - 59387 3 chr1 65537 74417 + 58860 4 chr1 65537 74417 + 59387 Actual Chromosome Start End Strand Distance 0 chr1 65537 71530 - 58860 1 chr1 65537 71530 - 59387 2 chr1 65537 74417 + 58860 3 chr1 65537 74417 + 59387 Expected Chromosome Start End Strand Distance 0 chr1 65537 71530 - 58860 1 chr1 65537 71530 - 59387 2 chr1 65537 74417 + 58860 3 chr1 65537 74417 + 59387 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9bnh5svd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9bnh5svd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 65537 71530 - 58860 2 chr1 65537 71530 - 59387 3 chr1 65537 74417 + 58860 4 chr1 65537 74417 + 59387 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 74417 | a | 0 | ... | | chr1 | 65537 | 74417 | a | 0 | ... | | chr1 | 65537 | 71530 | a | 0 | ... | | chr1 | 65537 | 71530 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 65537 71530 - 58860 3 chr1 65537 71530 - 59387 0 chr1 65537 74417 + 58860 1 chr1 65537 74417 + 59387 df2 Chromosome Start End Strand Distance 1 chr1 65537 71530 - 58860 2 chr1 65537 71530 - 59387 3 chr1 65537 74417 + 58860 4 chr1 65537 74417 + 59387 Actual Chromosome Start End Strand Distance 0 chr1 65537 71530 - 58860 1 chr1 65537 71530 - 59387 2 chr1 65537 74417 + 58860 3 chr1 65537 74417 + 59387 Expected Chromosome Start End Strand Distance 0 chr1 65537 71530 - 58860 1 chr1 65537 71530 - 59387 2 chr1 65537 74417 + 58860 3 chr1 65537 74417 + 59387 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpidbayk6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidbayk6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 4 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 6 chr1 6939432 6943449 - 2578136 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1553049 | 1557795 | a | 0 | ... | | chr1 | 2796697 | 2804841 | a | 0 | ... | | chr1 | 9252510 | 9259614 | a | 0 | ... | | chr1 | 2963787 | 2965287 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 8894 | a | 0 | ... | | chr1 | 4910128 | 4918617 | a | 0 | ... | | chr1 | 9251337 | 9252190 | a | 0 | ... | | chr1 | 6939432 | 6943449 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 8894 + 9512691 0 chr1 1553049 1557795 + 7963790 1 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 7 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 9 chr1 6939432 6943449 - 2578136 4 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 2 chr1 9252510 9259614 + 261971 df2 Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 4 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 6 chr1 6939432 6943449 - 2578136 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Actual Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 4 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 6 chr1 6939432 6943449 - 2578136 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Expected Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 4 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 6 chr1 6939432 6943449 - 2578136 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb3vfs3tz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3vfs3tz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2052031 2056048 - 7465537 3 chr1 2796697 2804841 + 6716744 4 chr1 2963787 2965287 + 6556298 5 chr1 4910128 4918617 + 4602968 6 chr1 6714337 6723230 + 2798355 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1553049 | 1557795 | a | 0 | ... | | chr1 | 2796697 | 2804841 | a | 0 | ... | | chr1 | 9252510 | 9259614 | a | 0 | ... | | chr1 | 2963787 | 2965287 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 8894 | a | 0 | ... | | chr1 | 4910128 | 4918617 | a | 0 | ... | | chr1 | 9251337 | 9252190 | a | 0 | ... | | chr1 | 2052031 | 2056048 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 8894 + 9512691 0 chr1 1553049 1557795 + 7963790 9 chr1 2052031 2056048 - 7465537 1 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 7 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 4 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 2 chr1 9252510 9259614 + 261971 df2 Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2052031 2056048 - 7465537 3 chr1 2796697 2804841 + 6716744 4 chr1 2963787 2965287 + 6556298 5 chr1 4910128 4918617 + 4602968 6 chr1 6714337 6723230 + 2798355 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Actual Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2052031 2056048 - 7465537 3 chr1 2796697 2804841 + 6716744 4 chr1 2963787 2965287 + 6556298 5 chr1 4910128 4918617 + 4602968 6 chr1 6714337 6723230 + 2798355 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Expected Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2052031 2056048 - 7465537 3 chr1 2796697 2804841 + 6716744 4 chr1 2963787 2965287 + 6556298 5 chr1 4910128 4918617 + 4602968 6 chr1 6714337 6723230 + 2798355 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp22y40lfe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp22y40lfe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppzcnrrxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppzcnrrxt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2419316 | 2427898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 df2 Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 Actual Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 Expected Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmpfnh2xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpfnh2xp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 2353777 1 chr1 2419316 2427898 - 2419310 2 chr1 9521584 9525796 - 9456045 3 chr1 9521584 9525796 - 9521578 4 chr1 9521584 9528114 + 9456045 5 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 8 chr1 9521584 9529908 + 9456045 9 chr1 9521584 9529908 + 9521578 10 chr1 9521584 9530197 + 9456045 11 chr1 9521584 9530197 + 9521578 12 chr16 5424116 5428005 + 5424113 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9521584 | 9528114 | a | 0 | ... | | chr1 | 9521584 | 9528114 | a | 0 | ... | | chr1 | 9521584 | 9530197 | a | 0 | ... | | chr1 | 9521584 | 9530197 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9521584 | 9525796 | a | 0 | ... | | chr1 | 9521584 | 9525796 | a | 0 | ... | | chr1 | 2419316 | 2427898 | a | 0 | ... | | chr1 | 2419316 | 2427898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 2419316 2427898 - 2353777 11 chr1 2419316 2427898 - 2419310 12 chr16 5424116 5428005 + 5424113 8 chr1 9521584 9525796 - 9456045 9 chr1 9521584 9525796 - 9521578 0 chr1 9521584 9528114 + 9456045 1 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 4 chr1 9521584 9529908 + 9456045 5 chr1 9521584 9529908 + 9521578 2 chr1 9521584 9530197 + 9456045 3 chr1 9521584 9530197 + 9521578 df2 Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 2353777 1 chr1 2419316 2427898 - 2419310 12 chr16 5424116 5428005 + 5424113 2 chr1 9521584 9525796 - 9456045 3 chr1 9521584 9525796 - 9521578 4 chr1 9521584 9528114 + 9456045 5 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 8 chr1 9521584 9529908 + 9456045 9 chr1 9521584 9529908 + 9521578 10 chr1 9521584 9530197 + 9456045 11 chr1 9521584 9530197 + 9521578 Actual Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 2353777 1 chr1 2419316 2427898 - 2419310 2 chr1 9521584 9525796 - 9456045 3 chr1 9521584 9525796 - 9521578 4 chr1 9521584 9528114 + 9456045 5 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 8 chr1 9521584 9529908 + 9456045 9 chr1 9521584 9529908 + 9521578 10 chr1 9521584 9530197 + 9456045 11 chr1 9521584 9530197 + 9521578 12 chr16 5424116 5428005 + 5424113 Expected Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 2353777 1 chr1 2419316 2427898 - 2419310 2 chr1 9521584 9525796 - 9456045 3 chr1 9521584 9525796 - 9521578 4 chr1 9521584 9528114 + 9456045 5 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 8 chr1 9521584 9529908 + 9456045 9 chr1 9521584 9529908 + 9521578 10 chr1 9521584 9530197 + 9456045 11 chr1 9521584 9530197 + 9521578 12 chr16 5424116 5428005 + 5424113 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpegnnw20a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegnnw20a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 1 chr1 9521584 9525796 - 7093687 2 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 4 chr1 9521584 9529908 + 7093687 5 chr1 9521584 9530197 + 7093687 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9521584 | 9528114 | a | 0 | ... | | chr1 | 9521584 | 9530197 | a | 0 | ... | | chr1 | 9521584 | 9529908 | a | 0 | ... | | chr1 | 9521584 | 9528166 | a | 0 | ... | | chr1 | 9521584 | 9525796 | a | 0 | ... | | chr1 | 2419316 | 2427898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 2419316 2427898 - 7093687 4 chr1 9521584 9525796 - 7093687 0 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 2 chr1 9521584 9529908 + 7093687 1 chr1 9521584 9530197 + 7093687 df2 Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 1 chr1 9521584 9525796 - 7093687 2 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 4 chr1 9521584 9529908 + 7093687 5 chr1 9521584 9530197 + 7093687 Actual Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 1 chr1 9521584 9525796 - 7093687 2 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 4 chr1 9521584 9529908 + 7093687 5 chr1 9521584 9530197 + 7093687 Expected Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 1 chr1 9521584 9525796 - 7093687 2 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 4 chr1 9521584 9529908 + 7093687 5 chr1 9521584 9530197 + 7093687 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm31ch_tv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm31ch_tv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 2 chr1 2037311 2038835 + 1858403 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2037311 | 2038835 | a | 0 | ... | | chr1 | 542815 | 542959 | a | 0 | ... | | chr1 | 1 | 10001 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 0 chr1 2037311 2038835 + 1858403 df2 Chromosome Start End Strand Distance 0 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 2 chr1 2037311 2038835 + 1858403 Actual Chromosome Start End Strand Distance 0 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 2 chr1 2037311 2038835 + 1858403 Expected Chromosome Start End Strand Distance 0 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 2 chr1 2037311 2038835 + 1858403 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb6js16ll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb6js16ll/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 10001 + 532815 1 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 4 chr1 2037311 2038835 + 1494353 5 chr1 2037311 2038835 + 2027311 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2037311 | 2038835 | a | 0 | ... | | chr1 | 2037311 | 2038835 | a | 0 | ... | | chr1 | 542815 | 542959 | a | 0 | ... | | chr1 | 542815 | 542959 | a | 0 | ... | | chr1 | 1 | 10001 | a | 0 | ... | | chr1 | 1 | 10001 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 10001 + 532815 5 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 0 chr1 2037311 2038835 + 1494353 1 chr1 2037311 2038835 + 2027311 df2 Chromosome Start End Strand Distance 0 chr1 1 10001 + 532815 1 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 4 chr1 2037311 2038835 + 1494353 5 chr1 2037311 2038835 + 2027311 Actual Chromosome Start End Strand Distance 0 chr1 1 10001 + 532815 1 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 4 chr1 2037311 2038835 + 1494353 5 chr1 2037311 2038835 + 2027311 Expected Chromosome Start End Strand Distance 0 chr1 1 10001 + 532815 1 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 4 chr1 2037311 2038835 + 1494353 5 chr1 2037311 2038835 + 2027311 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf0mmb0ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0mmb0ox/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 df2 Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6hagcynl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hagcynl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr17 | 4 | 5 | a | 0 | ... | | chr17 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr17 4 5 - 3 4 chr17 4 5 - 7235 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 df2 Chromosome Start End Strand Distance 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 3 chr17 4 5 - 3 4 chr17 4 5 - 7235 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 3 chr17 4 5 - 3 4 chr17 4 5 - 7235 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp27px9c53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp27px9c53/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr17 | 4 | 5 | a | 0 | ... | | chr17 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 df2 Chromosome Start End Strand Distance 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg8gmrvfx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8gmrvfx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsvkltc15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvkltc15/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6z338jis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6z338jis/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 1 chr1 2629111 2634771 + 1014858 2 chr1 2629111 2634771 + 864207 3 chr1 2629111 2634771 + 1014858 4 chr1 2629111 2634771 - 864207 5 chr1 2629111 2634771 - 1014858 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 2 chr1 2629111 2634771 + 864207 4 chr1 2629111 2634771 - 864207 1 chr1 2629111 2634771 + 1014858 3 chr1 2629111 2634771 + 1014858 5 chr1 2629111 2634771 - 1014858 df2 Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 2 chr1 2629111 2634771 + 864207 4 chr1 2629111 2634771 - 864207 1 chr1 2629111 2634771 + 1014858 3 chr1 2629111 2634771 + 1014858 5 chr1 2629111 2634771 - 1014858 Actual Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 1 chr1 2629111 2634771 + 864207 2 chr1 2629111 2634771 + 1014858 3 chr1 2629111 2634771 + 1014858 4 chr1 2629111 2634771 - 864207 5 chr1 2629111 2634771 - 1014858 Expected Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 1 chr1 2629111 2634771 + 864207 2 chr1 2629111 2634771 + 1014858 3 chr1 2629111 2634771 + 1014858 4 chr1 2629111 2634771 - 864207 5 chr1 2629111 2634771 - 1014858 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7xwz0o27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xwz0o27/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5660 5662 + 5380 1 chr1 5660 5917 + 5380 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5660 | 5917 | a | 0 | ... | | chr1 | 5660 | 5662 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 5660 5662 + 5380 0 chr1 5660 5917 + 5380 df2 Chromosome Start End Strand Distance 0 chr1 5660 5662 + 5380 1 chr1 5660 5917 + 5380 Actual Chromosome Start End Strand Distance 0 chr1 5660 5662 + 5380 1 chr1 5660 5917 + 5380 Expected Chromosome Start End Strand Distance 0 chr1 5660 5662 + 5380 1 chr1 5660 5917 + 5380 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv14z1ldx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv14z1ldx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65539 + 65257 1 chr1 65537 65794 + 65257 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 65537 65539 + 65257 0 chr1 65537 65794 + 65257 df2 Chromosome Start End Strand Distance 0 chr1 65537 65539 + 65257 1 chr1 65537 65794 + 65257 Actual Chromosome Start End Strand Distance 0 chr1 65537 65539 + 65257 1 chr1 65537 65794 + 65257 Expected Chromosome Start End Strand Distance 0 chr1 65537 65539 + 65257 1 chr1 65537 65794 + 65257 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkhcp1wg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkhcp1wg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 - 60353 4 chr2 65537 65539 - 60353 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 5183 | 5185 | a | 0 | ... | | chr2 | 65537 | 65539 | a | 0 | ... | | chr2 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 df2 Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 - 60353 4 chr2 65537 65539 - 60353 Actual Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 Expected Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb88kmlu6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb88kmlu6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 - 60353 4 chr2 65537 65539 - 60353 6 chrX 2348 2350 - 63188 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 5183 | 5185 | a | 0 | ... | | chr2 | 65537 | 65539 | a | 0 | ... | | chr2 | 65537 | 65539 | a | 0 | ... | | chrX | 2348 | 2350 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chrX 2348 2350 - 63188 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 df2 Chromosome Start End Strand Distance 6 chrX 2348 2350 - 63188 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 - 60353 4 chr2 65537 65539 - 60353 Actual Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 3 chrX 2348 2350 - 63188 Expected Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 3 chrX 2348 2350 - 63188 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwssd00k4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwssd00k4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 + 60353 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 65537 | 65539 | a | 0 | ... | | chr2 | 5183 | 5185 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr2 5183 5185 + 60353 0 chr2 65537 65539 + 60353 df2 Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 + 60353 Actual Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 + 60353 Expected Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 + 60353 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7a3n28p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7a3n28p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 5183 | 5185 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 df2 Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 Actual Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 Expected Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjddppi28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjddppi28/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4911929 | 4917782 | a | 0 | ... | | chr1 | 4911929 | 4917782 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 df2 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Actual Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Expected Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbxn9ca1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxn9ca1s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4911929 | 4917782 | a | 0 | ... | | chr1 | 4911929 | 4917782 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 df2 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Actual Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Expected Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjg5dii8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjg5dii8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4911929 | 4917782 | a | 0 | ... | | chr1 | 4911929 | 4917782 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 df2 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 Actual Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 Expected Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ndta1_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ndta1_b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 349416 | 349417 | a | 0 | ... | | chr1 | 6821752 | 6821753 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 df2 Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 Actual Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 Expected Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm0eoxlhk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0eoxlhk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 1 chr1 6821752 6821753 - 6821751 2 chr19 9614667 9614668 + 9614666 3 chr8 3816828 3816829 - 3816827 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 349416 | 349417 | a | 0 | ... | | chr1 | 6821752 | 6821753 | a | 0 | ... | | chr8 | 3816828 | 3816829 | a | 0 | ... | | chr19 | 9614667 | 9614668 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 2 chr8 3816828 3816829 - 3816827 1 chr1 6821752 6821753 - 6821751 3 chr19 9614667 9614668 + 9614666 df2 Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 3 chr8 3816828 3816829 - 3816827 1 chr1 6821752 6821753 - 6821751 2 chr19 9614667 9614668 + 9614666 Actual Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 1 chr1 6821752 6821753 - 6821751 2 chr19 9614667 9614668 + 9614666 3 chr8 3816828 3816829 - 3816827 Expected Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 1 chr1 6821752 6821753 - 6821751 2 chr19 9614667 9614668 + 9614666 3 chr8 3816828 3816829 - 3816827 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz8pk4g3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8pk4g3j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp63rz8t96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp63rz8t96/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfwcj193/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfwcj193/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4142043 | 4143301 | a | 0 | ... | | chr1 | 4142043 | 4143301 | a | 0 | ... | | chr1 | 1069717 | 1078872 | a | 0 | ... | | chr1 | 1069717 | 1078872 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9521805 | 9529666 | a | 0 | ... | | chr1 | 9521805 | 9529666 | a | 0 | ... | | chr1 | 6132725 | 6136874 | a | 0 | ... | | chr1 | 6132725 | 6136874 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1069717 1078872 - 6981140 3 chr1 1069717 1078872 - 8592821 0 chr1 4142043 4143301 + 3916711 1 chr1 4142043 4143301 + 5528392 6 chr1 4675618 4680602 - 3379410 7 chr1 4675618 4680602 - 4991091 10 chr1 6132725 6136874 - 1923138 11 chr1 6132725 6136874 - 3534819 4 chr1 7175802 7184372 - 875640 5 chr1 7175802 7184372 - 2487321 8 chr1 9521805 9529666 - 142027 9 chr1 9521805 9529666 - 1454608 df2 Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Actual Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Expected Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmd7a9uff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmd7a9uff/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4142043 | 4143301 | a | 0 | ... | | chr1 | 4142043 | 4143301 | a | 0 | ... | | chr1 | 1069717 | 1078872 | a | 0 | ... | | chr1 | 1069717 | 1078872 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9521805 | 9529666 | a | 0 | ... | | chr1 | 9521805 | 9529666 | a | 0 | ... | | chr1 | 6132725 | 6136874 | a | 0 | ... | | chr1 | 6132725 | 6136874 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1069717 1078872 - 6981140 3 chr1 1069717 1078872 - 8592821 0 chr1 4142043 4143301 + 3916711 1 chr1 4142043 4143301 + 5528392 6 chr1 4675618 4680602 - 3379410 7 chr1 4675618 4680602 - 4991091 10 chr1 6132725 6136874 - 1923138 11 chr1 6132725 6136874 - 3534819 4 chr1 7175802 7184372 - 875640 5 chr1 7175802 7184372 - 2487321 8 chr1 9521805 9529666 - 142027 9 chr1 9521805 9529666 - 1454608 df2 Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Actual Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Expected Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7pm_bowa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pm_bowa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1069717 | 1069723 | a | 0 | ... | | chr1 | 1069717 | 1069723 | a | 0 | ... | | chr1 | 4142043 | 4142044 | a | 0 | ... | | chr1 | 4142043 | 4142044 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 6 | a | 0 | ... | | chr1 | 2 | 6 | a | 0 | ... | | chr1 | 6132725 | 6132727 | a | 0 | ... | | chr1 | 6132725 | 6132727 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 2 5 - 65533 7 chr1 2 5 - 8060007 8 chr1 2 6 - 65532 9 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 0 chr1 1069717 1069723 + 1004180 1 chr1 1069717 1069723 + 6990289 2 chr1 4142043 4142044 - 3917968 3 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 df2 Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Actual Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Expected Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbyysqyno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbyysqyno/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1069717 | 1069723 | a | 0 | ... | | chr1 | 1069717 | 1069723 | a | 0 | ... | | chr1 | 4142043 | 4142044 | a | 0 | ... | | chr1 | 4142043 | 4142044 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 6 | a | 0 | ... | | chr1 | 2 | 6 | a | 0 | ... | | chr1 | 6132725 | 6132727 | a | 0 | ... | | chr1 | 6132725 | 6132727 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 2 5 - 65533 7 chr1 2 5 - 8060007 8 chr1 2 6 - 65532 9 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 0 chr1 1069717 1069723 + 1004180 1 chr1 1069717 1069723 + 6990289 2 chr1 4142043 4142044 - 3917968 3 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 df2 Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Actual Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Expected Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpew1qa50o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpew1qa50o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 5 2 chr1 5 6 - 1 3 chr1 5 6 - 2 4 chr1 5 7 - 2 5 chr1 5 8 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5 | 6 | a | 0 | ... | | chr1 | 5 | 6 | a | 0 | ... | | chr1 | 5 | 8 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 5 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1 2 - 5 0 chr1 5 6 - 1 1 chr1 5 6 - 2 4 chr1 5 7 - 2 2 chr1 5 8 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 5 2 chr1 5 6 - 1 3 chr1 5 6 - 2 4 chr1 5 7 - 2 5 chr1 5 8 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 5 1 chr1 5 6 - 1 2 chr1 5 6 - 2 3 chr1 5 7 - 2 4 chr1 5 8 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 5 1 chr1 5 6 - 1 2 chr1 5 6 - 2 3 chr1 5 7 - 2 4 chr1 5 8 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpma_yvdnd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma_yvdnd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 5 2 chr1 5 6 - 1 3 chr1 5 6 - 2 4 chr1 5 7 - 2 5 chr1 5 8 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5 | 6 | a | 0 | ... | | chr1 | 5 | 6 | a | 0 | ... | | chr1 | 5 | 8 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 5 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1 2 - 5 0 chr1 5 6 - 1 1 chr1 5 6 - 2 4 chr1 5 7 - 2 2 chr1 5 8 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 5 2 chr1 5 6 - 1 3 chr1 5 6 - 2 4 chr1 5 7 - 2 5 chr1 5 8 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 5 1 chr1 5 6 - 1 2 chr1 5 6 - 2 3 chr1 5 7 - 2 4 chr1 5 8 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 5 1 chr1 5 6 - 1 2 chr1 5 6 - 2 3 chr1 5 7 - 2 4 chr1 5 8 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxsiqdsh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsiqdsh9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65538 - 65529 4 chr1 65537 65538 - 65534 5 chr1 65537 65542 - 65529 6 chr1 65537 65542 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 65537 65538 - 65529 3 chr1 65537 65538 - 65534 0 chr1 65537 65542 - 65529 1 chr1 65537 65542 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 65537 65538 - 65529 4 chr1 65537 65538 - 65534 5 chr1 65537 65542 - 65529 6 chr1 65537 65542 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65529 1 chr1 65537 65538 - 65534 2 chr1 65537 65542 - 65529 3 chr1 65537 65542 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65529 1 chr1 65537 65538 - 65534 2 chr1 65537 65542 - 65529 3 chr1 65537 65542 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpemaduesg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpemaduesg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10006658 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 df2 Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 Actual Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 Expected Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphrk23wvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphrk23wvi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuocutwil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuocutwil/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqqel4p_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqel4p_v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0izf73n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0izf73n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6x8ln8bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6x8ln8bo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps6sk_6vk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6sk_6vk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1373867 | 1381103 | a | 0 | ... | | chr1 | 6955840 | 6956918 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 df2 Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 Actual Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 Expected Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5u4m9cj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5u4m9cj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1373867 | 1381103 | a | 0 | ... | | chr1 | 6955840 | 6956918 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 df2 Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 Actual Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 Expected Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvp5mk8i2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvp5mk8i2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 61 | 5170 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 df2 Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 Actual Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 Expected Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1z7c__pe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1z7c__pe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 106 107 - 65431 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 106 | 107 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 65536 0 chr1 106 107 - 65431 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 106 107 - 65431 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 106 107 - 65431 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 106 107 - 65431 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpikvxl74q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpikvxl74q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsem8xy3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsem8xy3w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3420973 | a | 0 | ... | | chr1 | 3420790 | 3420973 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmnsi0r7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmnsi0r7w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd537r946/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd537r946/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpehkf8zzm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehkf8zzm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2gcyuo2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gcyuo2c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgx7ueee4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgx7ueee4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9k92xs9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9k92xs9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 80 337 + 65201 1 chr1 65537 65794 + 65201 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 80 | 337 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 80 337 + 65201 0 chr1 65537 65794 + 65201 df2 Chromosome Start End Strand Distance 0 chr1 80 337 + 65201 1 chr1 65537 65794 + 65201 Actual Chromosome Start End Strand Distance 0 chr1 80 337 + 65201 1 chr1 65537 65794 + 65201 Expected Chromosome Start End Strand Distance 0 chr1 80 337 + 65201 1 chr1 65537 65794 + 65201 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm53qp1yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm53qp1yv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 557234 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 8 chr17 4069990 4079662 - 3688711 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4437037 | 4438637 | a | 0 | ... | | chr1 | 4437037 | 4438637 | a | 0 | ... | | chr1 | 9149560 | 9151160 | a | 0 | ... | | chr1 | 9149560 | 9151160 | a | 0 | ... | | chr1 | 4816435 | 4818035 | a | 0 | ... | | chr1 | 4816435 | 4818035 | a | 0 | ... | | chr13 | 282116 | 283716 | a | 0 | ... | | chr17 | 4069990 | 4079662 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 4 chr1 4816435 4818035 - 204998 5 chr1 4816435 4818035 - 557234 2 chr1 9149560 9151160 - 579776 3 chr1 9149560 9151160 - 4119439 df2 Chromosome Start End Strand Distance 6 chr13 282116 283716 + 2483040 8 chr17 4069990 4079662 - 3688711 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 557234 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 Actual Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 557234 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 Expected Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 557234 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvhpzy772/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvhpzy772/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 560011 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 8 chr17 4069990 4079662 - 3688711 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4437037 | 4438637 | a | 0 | ... | | chr1 | 4437037 | 4438637 | a | 0 | ... | | chr1 | 9149560 | 9151160 | a | 0 | ... | | chr1 | 9149560 | 9151160 | a | 0 | ... | | chr1 | 4816435 | 4818035 | a | 0 | ... | | chr1 | 4816435 | 4818035 | a | 0 | ... | | chr13 | 282116 | 283716 | a | 0 | ... | | chr17 | 4069990 | 4079662 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 4 chr1 4816435 4818035 - 204998 5 chr1 4816435 4818035 - 560011 2 chr1 9149560 9151160 - 579776 3 chr1 9149560 9151160 - 4119439 df2 Chromosome Start End Strand Distance 6 chr13 282116 283716 + 2483040 8 chr17 4069990 4079662 - 3688711 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 560011 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 Actual Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 560011 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 Expected Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 560011 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps58azpgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps58azpgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 4092 - 1383881 1 chr1 2 4092 - 3398906 2 chr1 1387972 1395206 - 1383881 3 chr1 1387972 1395206 - 2007792 4 chr1 3402997 3412438 + 838683 5 chr1 3402997 3412438 + 1610595 6 chr1 4251120 4256425 - 766608 7 chr1 4251120 4256425 - 838683 8 chr1 5023032 5030122 + 766608 9 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5023032 | 5030122 | a | 0 | ... | | chr1 | 5023032 | 5030122 | a | 0 | ... | | chr1 | 3402997 | 3412438 | a | 0 | ... | | chr1 | 3402997 | 3412438 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1387972 | 1395206 | a | 0 | ... | | chr1 | 1387972 | 1395206 | a | 0 | ... | | chr1 | 9730935 | 9734072 | a | 0 | ... | | chr1 | 9730935 | 9734072 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 2 4092 - 1383881 7 chr1 2 4092 - 3398906 8 chr1 1387972 1395206 - 1383881 9 chr1 1387972 1395206 - 2007792 2 chr1 3402997 3412438 + 838683 3 chr1 3402997 3412438 + 1610595 4 chr1 4251120 4256425 - 766608 5 chr1 4251120 4256425 - 838683 0 chr1 5023032 5030122 + 766608 1 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 df2 Chromosome Start End Strand Distance 0 chr1 2 4092 - 1383881 1 chr1 2 4092 - 3398906 2 chr1 1387972 1395206 - 1383881 3 chr1 1387972 1395206 - 2007792 4 chr1 3402997 3412438 + 838683 5 chr1 3402997 3412438 + 1610595 6 chr1 4251120 4256425 - 766608 7 chr1 4251120 4256425 - 838683 8 chr1 5023032 5030122 + 766608 9 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 Actual Chromosome Start End Strand Distance 0 chr1 2 4092 - 1383881 1 chr1 2 4092 - 3398906 2 chr1 1387972 1395206 - 1383881 3 chr1 1387972 1395206 - 2007792 4 chr1 3402997 3412438 + 838683 5 chr1 3402997 3412438 + 1610595 6 chr1 4251120 4256425 - 766608 7 chr1 4251120 4256425 - 838683 8 chr1 5023032 5030122 + 766608 9 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 Expected Chromosome Start End Strand Distance 0 chr1 2 4092 - 1383881 1 chr1 2 4092 - 3398906 2 chr1 1387972 1395206 - 1383881 3 chr1 1387972 1395206 - 2007792 4 chr1 3402997 3412438 + 838683 5 chr1 3402997 3412438 + 1610595 6 chr1 4251120 4256425 - 766608 7 chr1 4251120 4256425 - 838683 8 chr1 5023032 5030122 + 766608 9 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4tmfdppz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tmfdppz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3137 6274 - 1381699 1 chr1 3137 6274 - 3396724 2 chr1 4090 8180 - 1379793 3 chr1 4090 8180 - 3394818 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 6 chr1 7090 14180 + 2999 7 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 10 chr1 9441 18882 + 5350 11 chr1 9441 18882 + 1369091 12 chr11 10000000 10010000 + 8161694 13 chr13 2887 5774 - 2760982 14 chr17 4608 9216 - 367457 15 chr22 7243 14486 + 6606587 16 chr6 8488 16976 - 8607893 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7090 | 14180 | a | 0 | ... | | chr1 | 7090 | 14180 | a | 0 | ... | | chr1 | 9441 | 18882 | a | 0 | ... | | chr1 | 9441 | 18882 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr11 | 10000000 | 10010000 | a | 0 | ... | | chr13 | 2887 | 5774 | a | 0 | ... | | chr17 | 4608 | 9216 | a | 0 | ... | | chr22 | 7243 | 14486 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr13 2887 5774 - 2760982 10 chr1 3137 6274 - 1381699 11 chr1 3137 6274 - 3396724 6 chr1 4090 8180 - 1379793 7 chr1 4090 8180 - 3394818 15 chr17 4608 9216 - 367457 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 0 chr1 7090 14180 + 2999 1 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 16 chr22 7243 14486 + 6606587 12 chr6 8488 16976 - 8607893 2 chr1 9441 18882 + 5350 3 chr1 9441 18882 + 1369091 13 chr11 10000000 10010000 + 8161694 df2 Chromosome Start End Strand Distance 13 chr13 2887 5774 - 2760982 0 chr1 3137 6274 - 1381699 1 chr1 3137 6274 - 3396724 2 chr1 4090 8180 - 1379793 3 chr1 4090 8180 - 3394818 14 chr17 4608 9216 - 367457 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 6 chr1 7090 14180 + 2999 7 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 15 chr22 7243 14486 + 6606587 16 chr6 8488 16976 - 8607893 10 chr1 9441 18882 + 5350 11 chr1 9441 18882 + 1369091 12 chr11 10000000 10010000 + 8161694 Actual Chromosome Start End Strand Distance 0 chr1 3137 6274 - 1381699 1 chr1 3137 6274 - 3396724 2 chr1 4090 8180 - 1379793 3 chr1 4090 8180 - 3394818 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 6 chr1 7090 14180 + 2999 7 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 10 chr1 9441 18882 + 5350 11 chr1 9441 18882 + 1369091 12 chr11 10000000 10010000 + 8161694 13 chr13 2887 5774 - 2760982 14 chr17 4608 9216 - 367457 15 chr22 7243 14486 + 6606587 16 chr6 8488 16976 - 8607893 Expected Chromosome Start End Strand Distance 0 chr1 3137 6274 - 1381699 1 chr1 3137 6274 - 3396724 2 chr1 4090 8180 - 1379793 3 chr1 4090 8180 - 3394818 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 6 chr1 7090 14180 + 2999 7 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 10 chr1 9441 18882 + 5350 11 chr1 9441 18882 + 1369091 12 chr11 10000000 10010000 + 8161694 13 chr13 2887 5774 - 2760982 14 chr17 4608 9216 - 367457 15 chr22 7243 14486 + 6606587 16 chr6 8488 16976 - 8607893 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwuhinvce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwuhinvce/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10 12 + 7 1 chr1 10 12 + 65526 2 chr1 10 12 - 7 3 chr1 10 12 - 65526 4 chr1 4090 4092 - 4078 5 chr1 4090 4092 - 4087 6 chr1 9441 9443 - 9429 7 chr1 9441 9443 - 9438 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10 | 12 | a | 0 | ... | | chr1 | 10 | 12 | a | 0 | ... | | chr1 | 10 | 12 | a | 0 | ... | | chr1 | 10 | 12 | a | 0 | ... | | chr1 | 9441 | 9443 | a | 0 | ... | | chr1 | 9441 | 9443 | a | 0 | ... | | chr1 | 4090 | 4092 | a | 0 | ... | | chr1 | 4090 | 4092 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 10 12 + 7 2 chr1 10 12 - 7 1 chr1 10 12 + 65526 3 chr1 10 12 - 65526 6 chr1 4090 4092 - 4078 7 chr1 4090 4092 - 4087 4 chr1 9441 9443 - 9429 5 chr1 9441 9443 - 9438 df2 Chromosome Start End Strand Distance 0 chr1 10 12 + 7 2 chr1 10 12 - 7 1 chr1 10 12 + 65526 3 chr1 10 12 - 65526 4 chr1 4090 4092 - 4078 5 chr1 4090 4092 - 4087 6 chr1 9441 9443 - 9429 7 chr1 9441 9443 - 9438 Actual Chromosome Start End Strand Distance 0 chr1 10 12 + 7 1 chr1 10 12 + 65526 2 chr1 10 12 - 7 3 chr1 10 12 - 65526 4 chr1 4090 4092 - 4078 5 chr1 4090 4092 - 4087 6 chr1 9441 9443 - 9429 7 chr1 9441 9443 - 9438 Expected Chromosome Start End Strand Distance 0 chr1 10 12 + 7 1 chr1 10 12 + 65526 2 chr1 10 12 - 7 3 chr1 10 12 - 65526 4 chr1 4090 4092 - 4078 5 chr1 4090 4092 - 4087 6 chr1 9441 9443 - 9429 7 chr1 9441 9443 - 9438 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpauqi4cei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpauqi4cei/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 9441 9443 - 9405 2 chr1 9441 9443 - 9436 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9441 | 9443 | a | 0 | ... | | chr1 | 9441 | 9443 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9441 9443 - 9405 1 chr1 9441 9443 - 9436 df2 Chromosome Start End Strand Distance 1 chr1 9441 9443 - 9405 2 chr1 9441 9443 - 9436 Actual Chromosome Start End Strand Distance 0 chr1 9441 9443 - 9405 1 chr1 9441 9443 - 9436 Expected Chromosome Start End Strand Distance 0 chr1 9441 9443 - 9405 1 chr1 9441 9443 - 9436 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5cqnml5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5cqnml5b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa4cwomxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4cwomxv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 893138 900766 - 8252862 1 chr1 1977785 1980587 - 7173041 2 chr1 2137836 2141603 + 7012025 3 chr1 3011321 3015378 - 6138250 4 chr1 3011321 3017780 - 6135848 5 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 7 chr1 6038708 6042886 - 3110742 8 chr1 7061761 7070084 + 2083544 9 chr1 7418574 7419400 + 1734228 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7061761 | 7070084 | a | 0 | ... | | chr1 | 2137836 | 2141603 | a | 0 | ... | | chr1 | 7418574 | 7419400 | a | 0 | ... | | chr1 | 4585257 | 4586204 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5608261 | 5613316 | a | 0 | ... | | chr1 | 1977785 | 1980587 | a | 0 | ... | | chr1 | 3011321 | 3017780 | a | 0 | ... | | chr1 | 3011321 | 3015378 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 893138 900766 - 8252862 7 chr1 1977785 1980587 - 7173041 1 chr1 2137836 2141603 + 7012025 9 chr1 3011321 3015378 - 6138250 8 chr1 3011321 3017780 - 6135848 3 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 5 chr1 6038708 6042886 - 3110742 0 chr1 7061761 7070084 + 2083544 2 chr1 7418574 7419400 + 1734228 df2 Chromosome Start End Strand Distance 0 chr1 893138 900766 - 8252862 1 chr1 1977785 1980587 - 7173041 2 chr1 2137836 2141603 + 7012025 3 chr1 3011321 3015378 - 6138250 4 chr1 3011321 3017780 - 6135848 5 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 7 chr1 6038708 6042886 - 3110742 8 chr1 7061761 7070084 + 2083544 9 chr1 7418574 7419400 + 1734228 Actual Chromosome Start End Strand Distance 0 chr1 893138 900766 - 8252862 1 chr1 1977785 1980587 - 7173041 2 chr1 2137836 2141603 + 7012025 3 chr1 3011321 3015378 - 6138250 4 chr1 3011321 3017780 - 6135848 5 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 7 chr1 6038708 6042886 - 3110742 8 chr1 7061761 7070084 + 2083544 9 chr1 7418574 7419400 + 1734228 Expected Chromosome Start End Strand Distance 0 chr1 893138 900766 - 8252862 1 chr1 1977785 1980587 - 7173041 2 chr1 2137836 2141603 + 7012025 3 chr1 3011321 3015378 - 6138250 4 chr1 3011321 3017780 - 6135848 5 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 7 chr1 6038708 6042886 - 3110742 8 chr1 7061761 7070084 + 2083544 9 chr1 7418574 7419400 + 1734228 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3vuqjtmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vuqjtmv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7c0p289_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7c0p289_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2615129 2621642 + 2933057 3 chr1 2615129 2621642 + 7378359 8 chr1 5093094 5099699 - 455000 9 chr1 5093094 5099699 - 4900302 10 chr1 5532278 5536581 - 18118 11 chr1 5532278 5536581 - 4463420 0 chr1 7225386 7233529 + 1668099 1 chr1 7225386 7233529 + 2766472 6 chr1 8135388 8138430 - 1861571 7 chr1 8135388 8138430 - 2578101 12 chr1 8254305 8261673 - 1738328 13 chr1 8254305 8261673 - 2697018 4 chr1 9140426 9150079 + 849922 5 chr1 9140426 9150079 + 3583139 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqxy4vx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqxy4vx9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2615129 2621642 + 2933057 3 chr1 2615129 2621642 + 7378359 8 chr1 5093094 5099699 - 455000 9 chr1 5093094 5099699 - 4900302 10 chr1 5532278 5536581 - 18118 11 chr1 5532278 5536581 - 4463420 0 chr1 7225386 7233529 + 1668099 1 chr1 7225386 7233529 + 2766472 6 chr1 8135388 8138430 - 1861571 7 chr1 8135388 8138430 - 2578101 12 chr1 8254305 8261673 - 1738328 13 chr1 8254305 8261673 - 2697018 4 chr1 9140426 9150079 + 849922 5 chr1 9140426 9150079 + 3583139 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6mih4ewx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mih4ewx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2615129 2621642 + 2933057 3 chr1 2615129 2621642 + 7378359 8 chr1 5093094 5099699 - 455000 9 chr1 5093094 5099699 - 4900302 10 chr1 5532278 5536581 - 18118 11 chr1 5532278 5536581 - 4463420 0 chr1 7225386 7233529 + 1668099 1 chr1 7225386 7233529 + 2766472 6 chr1 8135388 8138430 - 1861571 7 chr1 8135388 8138430 - 2578101 12 chr1 8254305 8261673 - 1738328 13 chr1 8254305 8261673 - 2697018 4 chr1 9140426 9150079 + 849922 5 chr1 9140426 9150079 + 3583139 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5dxsb709/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5dxsb709/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 - 5466741 5 chr1 5532278 5536581 - 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 8135388 | 8138430 | a | 0 | ... | | chr1 | 8135388 | 8138430 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5093094 | 5099699 | a | 0 | ... | | chr1 | 5093094 | 5099699 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 2615129 2621642 - 2549592 9 chr1 2615129 2621642 - 2614872 10 chr1 5093094 5099699 - 5027557 11 chr1 5093094 5099699 - 5092837 12 chr1 5532278 5536581 - 5466741 13 chr1 5532278 5536581 - 5532021 0 chr1 7225386 7233529 + 7159849 1 chr1 7225386 7233529 + 7225129 2 chr1 8135388 8138430 + 8069851 3 chr1 8135388 8138430 + 8135131 6 chr1 8254305 8261673 + 8188768 7 chr1 8254305 8261673 + 8254048 4 chr1 9140426 9150079 + 9074889 5 chr1 9140426 9150079 + 9140169 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 - 5466741 5 chr1 5532278 5536581 - 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 - 5466741 5 chr1 5532278 5536581 - 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 - 5466741 5 chr1 5532278 5536581 - 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5k8z5_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5k8z5_y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 8135388 | 8138430 | a | 0 | ... | | chr1 | 8135388 | 8138430 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 5093094 | 5099699 | a | 0 | ... | | chr1 | 5093094 | 5099699 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 2615129 2621642 - 2549592 11 chr1 2615129 2621642 - 2614872 12 chr1 5093094 5099699 - 5027557 13 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 0 chr1 7225386 7233529 + 7159849 1 chr1 7225386 7233529 + 7225129 2 chr1 8135388 8138430 + 8069851 3 chr1 8135388 8138430 + 8135131 8 chr1 8254305 8261673 + 8188768 9 chr1 8254305 8261673 + 8254048 6 chr1 9140426 9150079 + 9074889 7 chr1 9140426 9150079 + 9140169 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkj9cv030/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkj9cv030/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65542 - 56211 4 chr1 65537 65542 - 65532 5 chr1 2615129 2615134 - 2605803 6 chr1 2615129 2615134 - 2615124 7 chr1 8135388 8135393 - 8126062 8 chr1 8135388 8135393 - 8135383 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8135388 | 8135393 | a | 0 | ... | | chr1 | 8135388 | 8135393 | a | 0 | ... | | chr1 | 2615129 | 2615134 | a | 0 | ... | | chr1 | 2615129 | 2615134 | a | 0 | ... | | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65542 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 65537 65542 - 56211 5 chr1 65537 65542 - 65532 2 chr1 2615129 2615134 - 2605803 3 chr1 2615129 2615134 - 2615124 0 chr1 8135388 8135393 - 8126062 1 chr1 8135388 8135393 - 8135383 df2 Chromosome Start End Strand Distance 3 chr1 65537 65542 - 56211 4 chr1 65537 65542 - 65532 5 chr1 2615129 2615134 - 2605803 6 chr1 2615129 2615134 - 2615124 7 chr1 8135388 8135393 - 8126062 8 chr1 8135388 8135393 - 8135383 Actual Chromosome Start End Strand Distance 0 chr1 65537 65542 - 56211 1 chr1 65537 65542 - 65532 2 chr1 2615129 2615134 - 2605803 3 chr1 2615129 2615134 - 2615124 4 chr1 8135388 8135393 - 8126062 5 chr1 8135388 8135393 - 8135383 Expected Chromosome Start End Strand Distance 0 chr1 65537 65542 - 56211 1 chr1 65537 65542 - 65532 2 chr1 2615129 2615134 - 2605803 3 chr1 2615129 2615134 - 2615124 4 chr1 8135388 8135393 - 8126062 5 chr1 8135388 8135393 - 8135383 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvsu86_n0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsu86_n0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65512 1 chr1 65537 65538 - 65512 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65542 + 65512 5 chr1 65537 65794 - 65512 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65538 - 65512 5 chr1 65537 65538 - 65512 0 chr1 65537 65542 + 65512 1 chr1 65537 65794 - 65512 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65512 1 chr1 65537 65538 - 65512 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65542 + 65512 5 chr1 65537 65794 - 65512 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65512 1 chr1 65537 65538 - 65512 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65542 + 65512 5 chr1 65537 65794 - 65512 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65512 1 chr1 65537 65538 - 65512 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65542 + 65512 5 chr1 65537 65794 - 65512 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7nmlzxuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nmlzxuc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 428464 | 433767 | a | 0 | ... | | chr1 | 4109934 | 4118195 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 df2 Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 Actual Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 Expected Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppjnioyqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjnioyqd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr10 6122965 6130048 + 2570271 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr10 | 6122965 | 6130048 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr10 6122965 6130048 + 2570271 df2 Chromosome Start End Strand Distance 2 chr10 6122965 6130048 + 2570271 Actual Chromosome Start End Strand Distance 0 chr10 6122965 6130048 + 2570271 Expected Chromosome Start End Strand Distance 0 chr10 6122965 6130048 + 2570271 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnln66alb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnln66alb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpold6k63h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpold6k63h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9kjc0fj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9kjc0fj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3px2hz_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3px2hz_0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2vn9mc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2vn9mc5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbmvy4u5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmvy4u5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1894566 1895027 - 1771318 1 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 4 chr1 7774529 7776683 + 732921 5 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 8 chr1 9999999 10002153 - 962584 9 chr1 9999999 10002153 - 2958391 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7774529 | 7776683 | a | 0 | ... | | chr1 | 7774529 | 7776683 | a | 0 | ... | | chr1 | 7757937 | 7767509 | a | 0 | ... | | chr1 | 7757937 | 7767509 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7835770 | 7839870 | a | 0 | ... | | chr1 | 7835770 | 7839870 | a | 0 | ... | | chr1 | 1894566 | 1895027 | a | 0 | ... | | chr1 | 1894566 | 1895027 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1894566 1895027 - 1771318 9 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 0 chr1 7774529 7776683 + 732921 1 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 4 chr1 9999999 10002153 - 962584 5 chr1 9999999 10002153 - 2958391 df2 Chromosome Start End Strand Distance 0 chr1 1894566 1895027 - 1771318 1 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 4 chr1 7774529 7776683 + 732921 5 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 8 chr1 9999999 10002153 - 962584 9 chr1 9999999 10002153 - 2958391 Actual Chromosome Start End Strand Distance 0 chr1 1894566 1895027 - 1771318 1 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 4 chr1 7774529 7776683 + 732921 5 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 8 chr1 9999999 10002153 - 962584 9 chr1 9999999 10002153 - 2958391 Expected Chromosome Start End Strand Distance 0 chr1 1894566 1895027 - 1771318 1 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 4 chr1 7774529 7776683 + 732921 5 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 8 chr1 9999999 10002153 - 962584 9 chr1 9999999 10002153 - 2958391 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwe5ctwxy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwe5ctwxy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7774529 7774786 - 7774519 3 chr1 7835770 7836027 - 7835760 4 chr1 9999999 10000256 - 9999989 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7774529 | 7774786 | a | 0 | ... | | chr1 | 9999999 | 10000256 | a | 0 | ... | | chr1 | 7835770 | 7836027 | a | 0 | ... | | chr1 | 7757937 | 7758194 | a | 0 | ... | | chr1 | 1894566 | 1894823 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1894566 1894823 - 1894556 3 chr1 7757937 7758194 - 7757927 0 chr1 7774529 7774786 - 7774519 2 chr1 7835770 7836027 - 7835760 1 chr1 9999999 10000256 - 9999989 df2 Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7774529 7774786 - 7774519 3 chr1 7835770 7836027 - 7835760 4 chr1 9999999 10000256 - 9999989 Actual Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7774529 7774786 - 7774519 3 chr1 7835770 7836027 - 7835760 4 chr1 9999999 10000256 - 9999989 Expected Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7774529 7774786 - 7774519 3 chr1 7835770 7836027 - 7835760 4 chr1 9999999 10000256 - 9999989 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe261jo8u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe261jo8u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 3 chr1 9399417 9399674 - 9399407 4 chr1 9999999 10000256 - 9999989 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9399417 | 9399674 | a | 0 | ... | | chr1 | 9999999 | 10000256 | a | 0 | ... | | chr1 | 7835770 | 7836027 | a | 0 | ... | | chr1 | 7757937 | 7758194 | a | 0 | ... | | chr1 | 1894566 | 1894823 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1894566 1894823 - 1894556 3 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 0 chr1 9399417 9399674 - 9399407 1 chr1 9999999 10000256 - 9999989 df2 Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 3 chr1 9399417 9399674 - 9399407 4 chr1 9999999 10000256 - 9999989 Actual Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 3 chr1 9399417 9399674 - 9399407 4 chr1 9999999 10000256 - 9999989 Expected Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 3 chr1 9399417 9399674 - 9399407 4 chr1 9999999 10000256 - 9999989 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyazptldz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyazptldz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65527 1 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 3 chr1 9999999 10000256 - 9999989 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9999999 | 10000256 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 7757937 | 7758194 | a | 0 | ... | | chr1 | 1894566 | 1894823 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 65537 65794 - 65527 3 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 0 chr1 9999999 10000256 - 9999989 df2 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65527 1 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 3 chr1 9999999 10000256 - 9999989 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65527 1 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 3 chr1 9999999 10000256 - 9999989 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65527 1 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 3 chr1 9999999 10000256 - 9999989 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2fga1zs_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2fga1zs_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr3 | 2684509 | 2691332 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 df2 Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Actual Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Expected Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn7vkwqyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7vkwqyn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr3 | 2684509 | 2691332 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 df2 Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Actual Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Expected Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp1orupya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1orupya/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6i_76cg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i_76cg6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3dcy9juz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dcy9juz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4177261 | 4184084 | a | 0 | ... | | chr1 | 4177261 | 4184084 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 df2 Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 Actual Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 Expected Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcihf6sjp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcihf6sjp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpot1t3u5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpot1t3u5u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi8_kb4c4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8_kb4c4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzcuxlu6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzcuxlu6r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4pkyqoay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pkyqoay/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1tyvb96j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tyvb96j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 6 - 2 2 chr1 3 7 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 5 chr1 65537 65540 + 65533 6 chr1 65537 65540 + 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 3 6 - 2 6 chr1 3 7 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 0 chr1 65537 65540 + 65533 1 chr1 65537 65540 + 65536 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 7 - 2 0 chr1 3 1284 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 5 chr1 65537 65540 + 65533 6 chr1 65537 65540 + 65536 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 7 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 5 chr1 65537 65540 + 65533 6 chr1 65537 65540 + 65536 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 7 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 5 chr1 65537 65540 + 65533 6 chr1 65537 65540 + 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbd6vzcnk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbd6vzcnk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 97 100 - 96 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 100 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 100 - 96 df2 Chromosome Start End Strand Distance 4 chr1 97 100 - 96 Actual Chromosome Start End Strand Distance 0 chr1 97 100 - 96 Expected Chromosome Start End Strand Distance 0 chr1 97 100 - 96 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplqv7txog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqv7txog/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 9 | a | 0 | ... | | chr1 | 3 | 9 | a | 0 | ... | | chr1 | 3 | 9 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 65537 | 65543 | a | 0 | ... | | chr1 | 65537 | 65543 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 df2 Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qj5zfy0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qj5zfy0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 6 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 4 chr1 3 6 - 2 0 chr1 3 1284 - 2 7 chr1 3 1284 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 1284 - 2 3 chr1 3 1284 - 2 4 chr1 97 104 - 90 5 chr1 97 104 - 96 6 chr1 65537 66818 - 65274 7 chr1 65537 66818 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnojrjshb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnojrjshb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 4 chr1 3 6 - 2 7 chr1 3 260 - 2 0 chr1 3 1284 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 260 - 2 0 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 1284 - 2 4 chr1 97 104 - 90 5 chr1 97 104 - 96 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_r_aibpw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_r_aibpw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 3 chr1 3 1284 - 2 6 chr1 3 1284 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 4 chr1 65537 66818 - 65274 5 chr1 65537 66818 - 65530 df2 Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplsqu41zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplsqu41zj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 6 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 4 chr1 3 6 - 2 0 chr1 3 1284 - 2 7 chr1 3 1284 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 1284 - 2 3 chr1 3 1284 - 2 4 chr1 97 104 - 90 5 chr1 97 104 - 96 6 chr1 65537 66818 - 65274 7 chr1 65537 66818 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5o19k841/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5o19k841/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 65537 66818 + 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 66818 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 66818 + 65280 df2 Chromosome Start End Strand Distance 4 chr1 65537 66818 + 65280 Actual Chromosome Start End Strand Distance 0 chr1 65537 66818 + 65280 Expected Chromosome Start End Strand Distance 0 chr1 65537 66818 + 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphcjbyggl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcjbyggl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 97 104 - 94 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 97 104 - 94 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgfq1t095/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfq1t095/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 4 chr1 3 6 - 2 0 chr1 3 260 - 2 7 chr1 3 260 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 0 chr1 3 260 - 2 1 chr1 3 260 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 97 104 - 90 5 chr1 97 104 - 96 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48dqbaae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48dqbaae/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpct1fsxf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpct1fsxf1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 97 104 - 94 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 97 104 - 94 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwki_0gef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwki_0gef/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 97 98 - 94 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 98 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 97 98 - 94 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprzugkoid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzugkoid/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 97 98 - 94 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 98 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 97 98 - 94 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz4ncki89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4ncki89/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 97 | 98 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 97 98 - 94 0 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgecuonuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgecuonuf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 97 | 98 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 97 98 - 94 0 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjyi9jm4l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjyi9jm4l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 6 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 260 - 2 5 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5hj3_hvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hj3_hvm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 6 chr1 3 260 - 2 0 chr1 65537 65544 - 65274 1 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 65537 65544 - 65274 3 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpujvngp00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujvngp00/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 6 chr1 3 260 - 2 0 chr1 65537 65544 - 65274 1 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 65537 65544 - 65274 3 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6o8jmity/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6o8jmity/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 6 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 260 - 2 5 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkk4nya4l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkk4nya4l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 65537 65794 - 65274 3 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=4, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqasyyght/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqasyyght/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 6 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 0 chr1 65537 65544 - 65274 1 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjludgqq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjludgqq2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg42n53ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg42n53ox/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 6 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 0 chr1 65537 65544 - 65274 1 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmmh3payb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmh3payb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5vy5jfgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vy5jfgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 4 - 4 2 chr1 65537 65540 - 65274 3 chr1 65537 65540 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65274 9 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 6 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 1 4 - 4 2 chr1 65537 65540 - 65274 3 chr1 65537 65540 - 65530 4 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65274 8 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 9 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphm19fjg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphm19fjg1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 7 chr1 65537 65538 - 65274 8 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 7 chr1 65537 65538 - 65274 8 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_qx5l13z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_qx5l13z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps6mrxj9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6mrxj9i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqax9z7lj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqax9z7lj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaz4skdux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaz4skdux/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 6 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 6 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvixru43y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvixru43y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 6 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 6 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcwpqysnu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcwpqysnu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 8 chr1 65537 65538 - 65274 9 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 8 chr1 65537 65538 - 65274 9 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp33wmvhx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33wmvhx7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 4 - 4 2 chr1 65537 65540 - 65274 3 chr1 65537 65540 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65274 9 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 6 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 1 4 - 4 2 chr1 65537 65540 - 65274 3 chr1 65537 65540 - 65530 4 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65274 8 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 9 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7525auod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7525auod/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 0 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 1 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjebsoakf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjebsoakf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 1 chr1 1 258 - 65280 2 chr1 65537 65538 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 2 chr1 1 258 - 65280 1 chr1 65537 65538 - 65530 df2 Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 1 chr1 1 258 - 65280 2 chr1 65537 65538 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 1 chr1 1 258 - 65280 2 chr1 65537 65538 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 1 chr1 1 258 - 65280 2 chr1 65537 65538 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp59lrvcp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59lrvcp3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_l8rtfss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_l8rtfss/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 6 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 6 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzvl5wd6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvl5wd6m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_oan8omu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_oan8omu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwjnpyrsh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjnpyrsh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptj863v68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj863v68/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbgy0xqmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgy0xqmh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 6 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 6 0 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 6 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyvrurw5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvrurw5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 6 chr1 65537 65538 - 65530 7 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 6 chr1 65537 65538 - 65530 7 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxrhbl6vt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrhbl6vt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 5 - 2 8 chr1 3 5 - 3 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 4 - 2 4 chr1 3 4 - 4 0 chr1 3 5 - 2 1 chr1 3 5 - 3 2 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 5 - 2 8 chr1 3 5 - 3 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1_kvkjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1_kvkjv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 8 - 6 6 chr1 7 9 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7 | 9 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 8 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 7 8 - 6 0 chr1 7 9 - 6 1 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 df2 Chromosome Start End Strand Distance 5 chr1 7 8 - 6 6 chr1 7 9 - 6 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 Actual Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 Expected Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_onf1khi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_onf1khi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpssnofkm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssnofkm_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0kfvrjb1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kfvrjb1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 7 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 6 0 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 7 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnasov08e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnasov08e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 7 chr1 65537 65538 - 65530 8 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 7 chr1 65537 65538 - 65530 8 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn1wxg241/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn1wxg241/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 8 - 6 7 chr1 7 9 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 9 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 8 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 7 8 - 6 1 chr1 7 9 - 6 0 chr1 7 264 - 6 2 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 df2 Chromosome Start End Strand Distance 6 chr1 7 8 - 6 7 chr1 7 9 - 6 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 Actual Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 Expected Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1_q1z8m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1_q1z8m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 7 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 6 0 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 7 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxn1movev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxn1movev/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf37an2hk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf37an2hk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyvqpl_i9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvqpl_i9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcgeu_dkz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgeu_dkz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_a7h08w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_a7h08w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkxhh3wr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkxhh3wr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplg5ed1zg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplg5ed1zg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpop8l8h6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpop8l8h6r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaqk8xsp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaqk8xsp3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 10 - 2 0 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_aj90xxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_aj90xxr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36c72hb7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36c72hb7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_iyvavfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_iyvavfn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpasr_7fio/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasr_7fio/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 4 - 2 8 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 4 - 2 4 chr1 3 4 - 4 1 chr1 3 10 - 2 0 chr1 3 260 - 2 2 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 4 - 2 8 chr1 3 4 - 4 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimkqjxym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimkqjxym/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 4 - 2 7 chr1 3 4 - 4 8 chr1 3 5 - 2 9 chr1 3 5 - 3 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 3 4 - 2 5 chr1 3 4 - 4 1 chr1 3 5 - 2 2 chr1 3 5 - 3 0 chr1 3 260 - 2 3 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 4 - 2 7 chr1 3 4 - 4 8 chr1 3 5 - 2 9 chr1 3 5 - 3 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp630o6lfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp630o6lfc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 8 - 6 7 chr1 7 9 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 9 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 8 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 7 8 - 6 1 chr1 7 9 - 6 0 chr1 7 264 - 6 2 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 df2 Chromosome Start End Strand Distance 6 chr1 7 8 - 6 7 chr1 7 9 - 6 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 Actual Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 Expected Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4zm3l2vi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zm3l2vi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 df2 Chromosome Start End Strand Distance 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclwrpk4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclwrpk4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2odrtmsb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2odrtmsb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_7gbtof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_7gbtof/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplbg2dakd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbg2dakd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcyknv7c_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcyknv7c_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2yrmhct5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2yrmhct5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpas1wqocw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas1wqocw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqgtok5do/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqgtok5do/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxybswc06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxybswc06/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2up0e4r7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2up0e4r7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp72cjzuwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72cjzuwy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 10 - 65528 2 chr1 3 260 - 2 3 chr1 3 260 - 65278 4 chr1 3 260 - 2 5 chr1 3 260 - 65278 6 chr1 3 260 - 2 7 chr1 3 260 - 65278 8 chr1 3 260 - 2 9 chr1 3 260 - 65278 10 chr1 3 260 - 2 11 chr1 3 260 - 65278 12 chr1 3 260 - 2 13 chr1 3 260 - 65278 14 chr1 3 6 - 2 15 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 3 6 - 2 5 chr1 3 6 - 65532 2 chr1 3 10 - 2 3 chr1 3 10 - 65528 0 chr1 3 260 - 2 6 chr1 3 260 - 2 8 chr1 3 260 - 2 10 chr1 3 260 - 2 12 chr1 3 260 - 2 14 chr1 3 260 - 2 1 chr1 3 260 - 65278 7 chr1 3 260 - 65278 9 chr1 3 260 - 65278 11 chr1 3 260 - 65278 13 chr1 3 260 - 65278 15 chr1 3 260 - 65278 df2 Chromosome Start End Strand Distance 14 chr1 3 6 - 2 15 chr1 3 6 - 65532 0 chr1 3 10 - 2 1 chr1 3 10 - 65528 2 chr1 3 260 - 2 4 chr1 3 260 - 2 6 chr1 3 260 - 2 8 chr1 3 260 - 2 10 chr1 3 260 - 2 12 chr1 3 260 - 2 3 chr1 3 260 - 65278 5 chr1 3 260 - 65278 7 chr1 3 260 - 65278 9 chr1 3 260 - 65278 11 chr1 3 260 - 65278 13 chr1 3 260 - 65278 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 65532 2 chr1 3 10 - 2 3 chr1 3 10 - 65528 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 10 chr1 3 260 - 65278 11 chr1 3 260 - 65278 12 chr1 3 260 - 65278 13 chr1 3 260 - 65278 14 chr1 3 260 - 65278 15 chr1 3 260 - 65278 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 65532 2 chr1 3 10 - 2 3 chr1 3 10 - 65528 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 10 chr1 3 260 - 65278 11 chr1 3 260 - 65278 12 chr1 3 260 - 65278 13 chr1 3 260 - 65278 14 chr1 3 260 - 65278 15 chr1 3 260 - 65278 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc4khfd27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc4khfd27/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjybqxbdj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjybqxbdj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvw0lzw4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvw0lzw4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcwo5h8ks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcwo5h8ks/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 8 chr1 65537 65794 - 65530 9 chr1 65537 65794 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 df2 Chromosome Start End Strand Distance 8 chr1 65537 65794 - 65530 9 chr1 65537 65794 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo1ikt_1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1ikt_1d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 4 - 2 12 chr1 3 4 - 4 13 chr1 3 4 - 2 14 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 13 chr1 3 4 - 2 1 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 14 chr1 3 4 - 4 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 13 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 14 chr1 3 4 - 4 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 2 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 4 - 4 13 chr1 3 4 - 4 14 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 2 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 4 - 4 13 chr1 3 4 - 4 14 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=15, step=1) index equal [ True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnfm9oh9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfm9oh9u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq95bqopa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq95bqopa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 4 - 2 12 chr1 3 4 - 4 13 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 13 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 14 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 13 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 6 - 2 13 chr1 3 6 - 2 14 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 6 - 2 13 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=14, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2f7n6pc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f7n6pc5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 4 - 2 12 chr1 3 4 - 4 13 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 13 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 14 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 13 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 6 - 2 13 chr1 3 6 - 2 14 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 6 - 2 13 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=14, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpox7mzbkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpox7mzbkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_0vv_tay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_0vv_tay/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgikd0nuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgikd0nuc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ocvue02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ocvue02/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclqa17zr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclqa17zr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 6 - 2 11 chr1 3 6 - 2 12 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 6 - 2 11 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=12, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd10ia4a7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd10ia4a7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 6 - 2 11 chr1 3 6 - 2 12 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 6 - 2 11 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=12, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpasu3vwt3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasu3vwt3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 6 - 2 9 chr1 3 6 - 2 10 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 6 - 2 9 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=10, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq9yarz9g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9yarz9g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 6 chr1 3 6 - 2 7 chr1 3 6 - 2 8 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 6 chr1 3 6 - 2 7 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm_fq4_0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_fq4_0w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 6 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcz76jebg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcz76jebg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 6 - 2 3 chr1 3 6 - 2 4 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 6 - 2 3 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=4, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp01lzbr8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01lzbr8s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 + 65528 1 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppqt556cz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppqt556cz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 + 65528 1 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfrns4dy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfrns4dy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptbzuc4st/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbzuc4st/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3z_nnmdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3z_nnmdq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd3u9aaw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3u9aaw4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9wxnn9px/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9wxnn9px/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 3 chr1 1 2 - 6 1 chr1 65537 65538 - 65530 2 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfgc8ofv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgc8ofv9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmsaqz9ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsaqz9ig/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 3 chr1 65537 65538 - 65530 4 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 3 chr1 1 2 - 6 4 chr1 1 2 - 6 1 chr1 65537 65538 - 65530 2 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 3 chr1 65537 65538 - 65530 4 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 3 chr1 65537 65538 - 65530 4 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 3 chr1 65537 65538 - 65530 4 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoysf88io/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoysf88io/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 3 chr1 1 2 - 6 1 chr1 65537 65538 - 65530 2 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3ineciq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3ineciq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 3 chr1 1 2 - 6 1 chr1 65537 65538 - 65530 2 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj100fec8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj100fec8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 + 65528 1 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38aw2mi2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38aw2mi2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 + 65528 1 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptj5sk76e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj5sk76e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 3 chr1 3 4 - 2 1 chr1 3 4 - 4 4 chr1 3 4 - 4 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9jq4dl07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jq4dl07/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 260 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 3 chr1 3 4 - 2 1 chr1 3 4 - 4 4 chr1 3 4 - 4 2 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 0 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpehqdwh78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehqdwh78/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 6 - 2 3 chr1 3 6 - 2 4 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 6 - 2 3 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=4, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0m40ro6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0m40ro6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 3 chr1 3 4 - 2 1 chr1 3 4 - 4 4 chr1 3 4 - 4 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2qncc8_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qncc8_v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhq5w64v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhq5w64v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 2 chr1 1 2 - 6 1 chr1 1 3 - 5 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpavwsvtq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavwsvtq5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 5 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbv83ps7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbv83ps7q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfhjcdkht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfhjcdkht/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 2 chr1 1 2 - 6 1 chr1 1 3 - 5 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjqd7ezvj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqd7ezvj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 2 chr1 1 2 - 6 1 chr1 1 3 - 5 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoxtr4b8i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxtr4b8i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 6 0 chr1 3 4 - 2 1 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa48psvy1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa48psvy1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 6 0 chr1 3 4 - 2 1 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc2a_7mb8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2a_7mb8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 6 0 chr1 3 4 - 2 1 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf2dzugyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2dzugyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcl6nnglh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcl6nnglh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2yxcb_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2yxcb_7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8cg8nqyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8cg8nqyj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 2 5 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnqpa9oz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnqpa9oz2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gvsk0qj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gvsk0qj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6kpf2op6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kpf2op6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 2 5 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz23uovjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz23uovjj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 4 - 2 4 chr1 3 4 - 2 3 chr1 3 4 - 4 5 chr1 3 4 - 4 0 chr1 3 5 - 2 1 chr1 3 5 - 3 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps7_wyw2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps7_wyw2b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmf2whqfz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmf2whqfz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 6 0 chr1 3 4 - 2 1 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkyzx22ww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyzx22ww/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 - 4 df2 Chromosome Start End Strand Distance 0 chr2 1 2 - 4 Actual Chromosome Start End Strand Distance 0 chr2 1 2 - 4 Expected Chromosome Start End Strand Distance 0 chr2 1 2 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsai1nl_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsai1nl_t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm3hckwxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3hckwxt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_4jkwrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_4jkwrw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr1v01et6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1v01et6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprvl50v7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprvl50v7o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 2 5 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaipgmjbk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaipgmjbk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr2 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr2 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr2 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa25fs_fe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa25fs_fe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf19rjv5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf19rjv5i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2hw0qp0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hw0qp0e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9jvda47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9jvda47/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0wrpgus3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0wrpgus3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ahn1nod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ahn1nod/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ok96lkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ok96lkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. =============================== warnings summary =============================== tests/conftest.py:83 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/conftest.py:83: SyntaxWarning: invalid escape sequence '\s' sep="\s+", pyranges/__init__.py:18: 13 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/__init__.py:18: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources tests/test_binary.py:118: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:118: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:139: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:139: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:160: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:160: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:187: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:187: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:212: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:212: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:291: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:291: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:329: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:329: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:368: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:368: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:392: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:392: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:426: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:426: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:516: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:516: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:579: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:579: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) pyranges/methods/init.py:60: 60 warnings .pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py: 9 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 161834 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 159199 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_getset_attr.py: 3 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_io.py: 4 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_pickle.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 6 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 358 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 25984 warnings .pybuild/cpython3_3.12_pyranges/build/tests/windows/test_windows.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 8 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_count_overlaps.py: 1 warning /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:60: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. return {k: v for k, v in df.groupby(grpby_key)} pyranges/methods/init.py:189: 48 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 4556 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 2000 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 6773 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 7 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:189: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby("Chromosome") tests/test_do_not_error.py:46: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py:46: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:35: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:35: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:100: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:100: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:163: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:163: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:205: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:205: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:234: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:234: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:272: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:272: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:287: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:287: HypothesisDeprecationWarning: The return_value health check is deprecated, because this is always an error. @settings( tests/test_unary.py:315: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:315: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 8380 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 16531 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 17602 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/tostring2.py:31: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. df = pd.concat([plus, minus]) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 1368 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:3779: FutureWarning: The behavior of Series.replace (and DataFrame.replace) with CategoricalDtype is deprecated. In a future version, replace will only be used for cases that preserve the categories. To change the categories, use ser.cat.rename_categories instead. other.Strand = other.Strand.replace({"+": "-", "-": "+"}) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 3239 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 119 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 5773 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 1 warning /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:187: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby(["Chromosome", "Strand"]) .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1217804. 1221351. 1223357. 1223968. 1227319. 1228946. 1232031.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1336515. 1337055. 1338183. 1338436. 1338653. 1339812. 1340190. 1340365. 1340503. 1342156. 1342484. 1342758. 1349350.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1311924. 1312147. 1313592. 1315697. 1317450. 1321096. 1321984. 1323287. 1324691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1293708. 1293933. 1294199. 1294628. 1295008. 1295554. 1295938. 1296109. 1296280. 1296633. 1297933. 1298265. 1298421. 1299905. 1300068. 1300202. 1300692. 1302046. 1302975. 1305929. 1307156. 1307383. 1308018. 1309609.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1084506. 1085310. 1086012. 1087636. 1092294. 1092813. 1106127. 1106871. 1115075. 1116361.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1472089. 1477350. 1478745. 1479108. 1480936. 1482303. 1482662. 1485171. 1486235. 1486668. 1487914. 1490671. 1497848.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1255487. 1256335. 1257130. 1257310. 1262390. 1263569. 1264830. 1266290. 1267992. 1271637. 1273885.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1173926. 1174321. 1174489. 1175034. 1179333. 1179853. 1180340. 1180884. 1181815. 1182446. 1183047. 1184091. 1185864. 1196488. 1196716. 1197186. 1197935.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1281610. 1282010. 1282319. 1284090. 1285664. 1286278. 1286975. 1287299. 1287836. 1288037. 1290388. 1290555. 1290694. 1290953. 1291140. 1292029.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1353946. 1354106. 1354509. 1355752. 1356704. 1358794. 1361777.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1331536. 1331938. 1332806. 1333124. 1333379. 1335306.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1308720. 1308972. 1309851. 1311071. 1311677.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000169972.11' 'ENSG00000169972.11' 'ENSG00000169972.11' 'ENSG00000169972.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1373902. 1375495.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000175756.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1235041.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 818202. 819837.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000177757.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1435146. 1435821. 1437484. 1442882.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000179403.11' 'ENSG00000179403.11' 'ENSG00000179403.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1242646. 1243552. 1244275. 1244724. 1246722.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000184163.3' 'ENSG00000184163.3' 'ENSG00000184163.3' 'ENSG00000184163.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 65433. 65573. 71585.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186092.6' 'ENSG00000186092.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1211832. 1212138. 1212704. 1213785. 1214138.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186827.10' 'ENSG00000186827.10' 'ENSG00000186827.10' 'ENSG00000186827.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1203968. 1204236. 1204486. 1205680. 1206691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186891.13' 'ENSG00000186891.13' 'ENSG00000186891.13' 'ENSG00000186891.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 966614. 966803. 970423. 970601. 971006. 971208. 971523. 972150. 972424. 973010. 973326. 973640. 974051. 974364. 975108. 975865.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1001281. 1008279. 1013576. 1014540.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187608.9' 'ENSG00000187608.9' 'ENSG00000187608.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 924948. 925189. 925800. 926013. 930336. 931089. 935896. 939129. 939460. 940462. 941306. 943058. 943377. 944581.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 976269. 976641. 981029. 981173. 982093.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187642.9' 'ENSG00000187642.9' 'ENSG00000187642.9' 'ENSG00000187642.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 960800. 961750. 962478. 962917. 963253. 963504. 964008. 964180. 964530. 965715.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1020373. 1022462. 1034703. 1035324. 1040880. 1041397. 1041702. 1042162. 1043457. 1043732. 1044023. 1044257. 1044439. 1045277. 1045523. 1045876. 1046088. 1046349. 1046735. 1046957. 1047454. 1047687. 1047895. 1048365. 1049059. 1049451. 1049795. 1050037. 1050329. 1050591. 1050837. 1051043. 1051369. 1051645. 1051815. 1053977. 1054551. 1056118.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 999432. 1000172.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188290.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 944800. 945146. 945422. 945653. 946286. 947060. 948232. 948603. 951238. 952139. 952600. 953288. 953892. 954523. 956013. 956215. 957025. 959081. 959309.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1512473. 1516088. 1517412. 1517775. 1518990. 1520306. 1520617.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 634922.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1169087.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1426385. 1427787.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000205116.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1176396. 1179555.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000205231.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1167952.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1167198.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1450758. 1452122. 1452434. 1454500. 1455519. 1455916. 1456349. 1457180. 1459231. 1460917. 1462708. 1470158.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1059846. 1060393. 1061117. 1063201. 1063566. 1064401. 1064589. 1065475. 1066456. 1066667. 1067646. 1068003. 1068724. 1069355.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1387582. 1387869. 1388743. 1388830. 1389047. 1389473. 1390371. 1390563. 1392803. 1393460. 1395537. 1398366. 1398956. 1399328.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 157887.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 758336.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1379032.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 921016.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1137110. 1141032. 1144056.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000223823.1' 'ENSG00000223823.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 12227. 12721. 13052. 14409.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000223972.5' 'ENSG00000223972.5' 'ENSG00000223972.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1325102. 1325595. 1327032. 1328897.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000224051.6' 'ENSG00000224051.6' 'ENSG00000224051.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1402046.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1012190. 1013193.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000224969.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1430954. 1431843. 1434573.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000225285.1' 'ENSG00000225285.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 630683.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 827522.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1420564. 1422691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000225905.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 629433.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 14501. 15038. 15947. 16765. 17055. 17368. 17742. 18061. 18366. 24891. 29570.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 729804. 733364. 735613. 743350. 744391. 744825. 746818. 756141. 759123. 765247. 766387. 768613. 769712. 773107. 774280. 778626.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 259025. 261634. 268204. 268816. 289370. 297502. 357586. 358183. 359681.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 825552. 826923. 827775. 827853. 829104. 831677. 842020. 847806. 849602. 850351. 852515. 852766. 859446.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 633438.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 724360. 724903.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000229376.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 761154. 761989.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000229905.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 586358. 586955. 588453. 594756. 598551. 601577. 608056. 612864. 627823. 628223. 629006. 631204. 633129. 698959. 702340. 703789. 711922. 720206. 724564. 732212. 733064. 827796.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 801163. 805891. 808623. 810170. 817712.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230092.7' 'ENSG00000230092.7' 'ENSG00000230092.7' 'ENSG00000230092.7']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 868675. 869575. 870201. 875155. 876903.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230368.2' 'ENSG00000230368.2' 'ENSG00000230368.2' 'ENSG00000230368.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1275299. 1279393. 1280420.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230415.1' 'ENSG00000230415.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 911473. 914948.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230699.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1008229.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 489387. 489906.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000233653.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 134836.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 874349.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1419549. 1420592. 1421769.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000235098.8' 'ENSG00000235098.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 587729. 594768.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000235146.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 358957. 360168. 366052.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000236601.2' 'ENSG00000236601.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 348366.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 365692. 366151. 368450. 373323. 379972. 476945. 485208. 489553. 494898. 495049. 495476. 496605. 497299. 498305. 499369. 501620. 502243. 502955. 505103. 514423. 517266. 522928.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1072575. 1074307.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237330.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 779092. 782191. 783363. 784977. 787672. 793041. 795582. 801876. 803667. 804222. 805270. 806459. 807465. 810060.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 35174. 35481. 36081.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237613.2' 'ENSG00000237613.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 632616.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 91629. 92240. 111357. 112804. 120932. 129223. 133723.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 139847. 140339.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000239906.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 90050. 91105.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000239945.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 57653. 58856. 64116.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000240361.2' 'ENSG00000240361.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 633741.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1317899. 1318689.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000240731.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 914444. 914971.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241180.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 160690. 161525.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241599.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 143011. 149707. 155831. 164791. 165942. 168165. 168767. 169264. 172688. 173862.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1402601. 1407019. 1407313.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000242485.5' 'ENSG00000242485.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1055215. 1056116.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000242590.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 30039. 30667. 31109.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000243485.5' 'ENSG00000243485.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 634376.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 491989. 493241.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000250575.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1251334.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1405752.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 53312.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 675265.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 135895.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 440232.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 137965.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1170343.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 904957. 915976.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000272438.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1410618.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 998051.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1062808. 1063288.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000273443.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 187958.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1296170.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 17436.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 516479.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 632413.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 185350. 185559. 186469. 187287. 187577. 187890. 188266. 188584. 188902. 195411.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 182746. 183216. 183571. 183901. 184174.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000279928.2' 'ENSG00000279928.2' 'ENSG00000279928.2' 'ENSG00000279928.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 874591. 875155. 875625. 876611. 877234.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000283040.1' 'ENSG00000283040.1' 'ENSG00000283040.1' 'ENSG00000283040.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1312566.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 30503.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1339708.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 686673.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 451697.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1503661. 1509452.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000284740.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 782050.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1098113. 1104598.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000285812.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:153: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. result_df.Cluster.replace(cluster_ids, inplace=True) .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for _, gdf in natsorted(df.groupby(groupby)): .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['+', '+', '-', NaN, NaN] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[NaN, NaN, NaN, '+', '-'] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] - ValueErr... ========= 1 failed, 530 passed, 418337 warnings in 4128.40s (1:08:48) ========== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 12 dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13 make: *** [debian/rules:22: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1596758 and its subdirectories Starting cleanup. All cleanup done. Fri Sep 27 02:47:14 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-7OrYZfFO, removing. /srv/reproducible-results/rbuild-debian/r-b-build.mqzlEEs2: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 02:47 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 27 01:37 b2 -rw-r--r-- 1 jenkins jenkins 2428 Sep 21 12:03 pyranges_0.0.111+ds-8.dsc -rw------- 1 jenkins jenkins 3568 Sep 27 01:37 rbuildlog.KoYaI3L /srv/reproducible-results/rbuild-debian/r-b-build.mqzlEEs2/b1: total 1856 -rw-r--r-- 1 jenkins jenkins 1898445 Sep 27 02:47 build.log /srv/reproducible-results/rbuild-debian/r-b-build.mqzlEEs2/b2: total 0 Fri Sep 27 02:47:15 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 26 13:37:07 -12 2024 I: pbuilder-time-stamp: 1727401027 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pyranges_0.0.111+ds-8.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Sep 21 11:53:08 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyranges_0.0.111+ds-8.dsc: no acceptable signature found dpkg-source: info: extracting pyranges in pyranges-0.0.111+ds dpkg-source: info: unpacking pyranges_0.0.111+ds.orig.tar.xz dpkg-source: info: unpacking pyranges_0.0.111+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_dtype.patch dpkg-source: info: applying reorder.patch dpkg-source: info: applying numpy_1.24.patch dpkg-source: info: applying healthcheck-all.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying pandas2.0.patch dpkg-source: info: applying fix-test_unary.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1596758/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='95b946540b07430d823bdeb3be0c2c6c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1596758' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.mqzlEEs2/pbuilderrc_lHEG --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mqzlEEs2/b1 --logfile b1/build.log pyranges_0.0.111+ds-8.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1596758/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-ncls, python3-pyrle, python3-pytest, python3-pytest-xdist, python3-sorted-nearest, python3-hypothesis, bedtools, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-ncls; however: Package python3-ncls is not installed. pbuilder-satisfydepends-dummy depends on python3-pyrle; however: Package python3-pyrle is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-sorted-nearest; however: Package python3-sorted-nearest is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-autocommand{a} python3-dateutil{a} python3-execnet{a} python3-hypothesis{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-natsort{a} python3-ncls{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyrle{a} python3-pytest{a} python3-pytest-xdist{a} python3-setuptools{a} python3-six{a} python3-sorted-nearest{a} python3-sortedcontainers{a} python3-tabulate{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-click python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget 0 packages upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After unpacking 211 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.5-1+b1 [26.9 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.5-1+b1 [9872 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.5-1+b1 [27.9 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 bedtools arm64 2.31.1+dfsg-2 [588 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240824 [109 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.10.1-1 [329 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-3 [362 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2 [95.7 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.5-1+b1 [1048 B] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-attr all 23.2.0-2 [65.5 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-7 [16.4 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-execnet all 2.1.1-1 [40.2 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-hypothesis all 6.112.0-1 [320 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-natsort all 8.0.2-2 [39.0 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-ncls arm64 0.0.63-hotfix+ds-1+b5 [339 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.2.2+dfsg-4+b1 [3571 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.2.2+dfsg-4 [3095 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 python3-pyrle arm64 0.0.33-4.1+b1 [263 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 python3-sorted-nearest arm64 0.0.39+dfsg-2+b1 [274 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3 [624 kB] Fetched 44.8 MB in 0s (124 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1+b1_arm64.deb ... Unpacking python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.5-1+b1) ... Setting up python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21289 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.5-1+b1_arm64.deb ... Unpacking python3 (3.12.5-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. 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Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../31-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../32-python3-more-itertools_10.4.0-1_all.deb ... Unpacking python3-more-itertools (10.4.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../33-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../34-python3-typeguard_4.3.0-1_all.deb ... Unpacking python3-typeguard (4.3.0-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../35-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../36-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. 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Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../49-libngtcp2-16_1.6.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../50-libngtcp2-crypto-gnutls8_1.6.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../51-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../52-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../53-libssh2-1t64_1.11.0-7_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-7) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../54-libcurl3t64-gnutls_8.10.1-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.10.1-1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../55-libdeflate0_1.21-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.21-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../56-libgfortran5_14.2.0-3_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-3) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../57-libhtscodecs2_1.6.1-1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.1-1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../58-libhts3t64_1.20+ds-1_arm64.deb ... Unpacking libhts3t64:arm64 (1.20+ds-1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../59-liblapack3_3.12.0-3_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../60-libncurses6_6.5-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5-2) ... Selecting previously unselected package python3-all. Preparing to unpack .../61-python3-all_3.12.5-1+b1_arm64.deb ... Unpacking python3-all (3.12.5-1+b1) ... Selecting previously unselected package python3-attr. Preparing to unpack .../62-python3-attr_23.2.0-2_all.deb ... Unpacking python3-attr (23.2.0-2) ... Selecting previously unselected package python3-six. Preparing to unpack .../63-python3-six_1.16.0-7_all.deb ... Unpacking python3-six (1.16.0-7) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../64-python3-dateutil_2.9.0-2_all.deb ... Unpacking python3-dateutil (2.9.0-2) ... Selecting previously unselected package python3-execnet. Preparing to unpack .../65-python3-execnet_2.1.1-1_all.deb ... Unpacking python3-execnet (2.1.1-1) ... Selecting previously unselected package python3-sortedcontainers. Preparing to unpack .../66-python3-sortedcontainers_2.4.0-2_all.deb ... Unpacking python3-sortedcontainers (2.4.0-2) ... Selecting previously unselected package python3-hypothesis. Preparing to unpack .../67-python3-hypothesis_6.112.0-1_all.deb ... Unpacking python3-hypothesis (6.112.0-1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../68-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-natsort. Preparing to unpack .../69-python3-natsort_8.0.2-2_all.deb ... Unpacking python3-natsort (8.0.2-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../70-python3-numpy_1%3a1.26.4+ds-11_arm64.deb ... Unpacking python3-numpy (1:1.26.4+ds-11) ... Selecting previously unselected package python3-ncls. Preparing to unpack .../71-python3-ncls_0.0.63-hotfix+ds-1+b5_arm64.deb ... Unpacking python3-ncls (0.0.63-hotfix+ds-1+b5) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../72-python3-packaging_24.1-1_all.deb ... Unpacking python3-packaging (24.1-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../73-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-pandas-lib:arm64. Preparing to unpack .../74-python3-pandas-lib_2.2.2+dfsg-4+b1_arm64.deb ... Unpacking python3-pandas-lib:arm64 (2.2.2+dfsg-4+b1) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../75-python3-pandas_2.2.2+dfsg-4_all.deb ... Unpacking python3-pandas (2.2.2+dfsg-4) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../76-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-tabulate. Preparing to unpack .../77-python3-tabulate_0.9.0-1_all.deb ... Unpacking python3-tabulate (0.9.0-1) ... Selecting previously unselected package python3-pyrle. Preparing to unpack .../78-python3-pyrle_0.0.33-4.1+b1_arm64.deb ... Unpacking python3-pyrle (0.0.33-4.1+b1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../79-python3-pytest_8.3.3-1_all.deb ... Unpacking python3-pytest (8.3.3-1) ... Selecting previously unselected package python3-pytest-xdist. Preparing to unpack .../80-python3-pytest-xdist_3.6.1-1_all.deb ... Unpacking python3-pytest-xdist (3.6.1-1) ... Selecting previously unselected package python3-sorted-nearest. Preparing to unpack .../81-python3-sorted-nearest_0.0.39+dfsg-2+b1_arm64.deb ... Unpacking python3-sorted-nearest (0.0.39+dfsg-2+b1) ... Selecting previously unselected package samtools. Preparing to unpack .../82-samtools_1.20-3_arm64.deb ... Unpacking samtools (1.20-3) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b4) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.63.0-1) ... Setting up libdeflate0:arm64 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Sep 27 01:37:42 UTC 2024. Universal Time is now: Fri Sep 27 01:37:42 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:arm64 (6.5-2) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-3) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.4.0-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libssh2-1t64:arm64 (1.11.0-7) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.10.1-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libhts3t64:arm64 (1.20+ds-1) ... Setting up libpython3.12-stdlib:arm64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:arm64 (3.12.5-1+b1) ... Setting up python3 (3.12.5-1+b1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-natsort (8.0.2-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-packaging (24.1-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-execnet (2.1.1-1) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-hypothesis (6.112.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.12.5-1+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-pytest-xdist (3.6.1-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b5) ... Setting up dh-python (6.20240824) ... Setting up python3-pandas-lib:arm64 (2.2.2+dfsg-4+b1) ... Setting up python3-sorted-nearest (0.0.39+dfsg-2+b1) ... Setting up python3-pandas (2.2.2+dfsg-4) ... Setting up python3-pyrle (0.0.33-4.1+b1) ... Processing triggers for libc-bin (2.40-2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-8_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyranges-0.0.111+ds' echo 'Generating corresponding files ...' Generating corresponding files ... cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai make[1]: Leaving directory '/build/reproducible-path/pyranges-0.0.111+ds' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/*.bed /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/test_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges '/build/reproducible-path/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/chip_10.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/gencode.gff3' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/exons.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/bw.bw' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/cpg.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/lamina.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam.bai' I: pybuild base:311: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 12 ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/.hypothesis/examples')) rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: xdist-3.6.1, hypothesis-6.112.0, typeguard-4.3.0 created: 12/12 workers 12 workers [531 items] scheduling tests via LoadScheduling tests/test_binary.py::test_coverage[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_nearest[None-False-opposite] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/data/test_data.py::test_all_data [gw0] [ 0%] PASSED tests/data/test_data.py::test_all_data tests/test_binary.py::test_set_intersect[False] [gw7] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] [gw6] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] [gw11] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] [gw9] [ 0%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] [gw5] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] [gw10] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] [gw7] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] [gw6] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] [gw10] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] [gw5] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] [gw9] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] [gw7] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] [gw6] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] [gw11] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] [gw7] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] [gw10] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] [gw5] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] [gw9] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] [gw6] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] [gw11] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] [gw10] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] [gw5] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] [gw7] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] [gw9] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] [gw6] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] [gw5] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] [gw10] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] [gw11] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] [gw6] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw7] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] [gw5] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] [gw10] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] [gw9] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] [gw11] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] [gw6] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw5] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] [gw7] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] [gw10] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] [gw9] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] [gw6] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] [gw5] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] [gw11] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] [gw10] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] [gw7] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] [gw9] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] [gw6] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] [gw5] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] [gw10] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] [gw6] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] [gw7] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] [gw11] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] [gw10] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] [gw9] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] [gw5] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] [gw6] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] [gw1] [ 10%] PASSED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_nearest[downstream-False-opposite] [gw10] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] [gw3] [ 11%] PASSED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_nearest[upstream-True-False] [gw5] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] [gw11] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw6] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] [gw9] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] [gw7] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] [gw10] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] [gw5] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] [gw11] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw6] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] [gw9] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] [gw10] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] [gw0] [ 13%] PASSED tests/test_binary.py::test_set_intersect[False] tests/test_binary.py::test_set_intersect[same] [gw7] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] [gw11] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] [gw6] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] [gw9] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] [gw7] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] [gw5] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw11] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] [gw2] [ 14%] PASSED tests/test_binary.py::test_coverage[False] [gw6] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_binary.py::test_coverage[same] [gw4] [ 15%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw10] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] [gw9] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] [gw7] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] [gw5] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw6] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] [gw11] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] [gw9] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] [gw7] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] [gw6] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] [gw10] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] [gw5] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] [gw9] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] [gw7] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] [gw11] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] [gw6] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] [gw7] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] [gw9] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] [gw10] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] [gw5] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] [gw11] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] [gw6] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] [gw7] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] [gw9] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] [gw5] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] [gw10] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] [gw7] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] [gw11] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] [gw6] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] [gw9] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] [gw7] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] [gw6] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] [gw11] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] [gw1] [ 21%] PASSED tests/test_binary.py::test_nearest[downstream-False-opposite] tests/test_binary.py::test_jaccard[False] [gw9] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] [gw5] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] [gw10] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] [gw11] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] [gw6] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] [gw7] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] [gw9] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw5] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw6] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] [gw11] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] [gw9] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] [gw10] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] [gw7] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] [gw5] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] [gw6] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] [gw11] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] [gw3] [ 24%] PASSED tests/test_binary.py::test_nearest[upstream-True-False] tests/test_binary.py::test_nearest[upstream-True-same] [gw7] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] [gw10] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] [gw6] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] [gw5] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] [gw11] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] [gw9] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] [gw6] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] [gw7] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] [gw0] [ 26%] PASSED tests/test_binary.py::test_set_intersect[same] tests/test_binary.py::test_set_union[False] [gw11] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] [gw10] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] [gw5] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] [gw7] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] [gw9] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] [gw6] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] [gw10] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] [gw5] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] [gw10] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] [gw7] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] [gw8] [ 28%] FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] [gw11] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw5] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] [gw9] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw6] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] [gw10] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] [gw7] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] [gw5] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] [gw10] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] [gw9] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] [gw7] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] [gw11] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] [gw6] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] [gw2] [ 30%] PASSED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_coverage[opposite] [gw9] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] [gw10] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] [gw7] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] [gw5] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] [gw11] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] [gw9] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw7] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] [gw10] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] [gw5] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] [gw6] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw9] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] [gw11] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] [gw4] [ 33%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw7] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw1] [ 33%] PASSED tests/test_binary.py::test_jaccard[False] tests/test_binary.py::test_jaccard[same] [gw10] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] [gw5] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] [gw7] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] [gw11] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw6] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] [gw9] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] [gw10] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] [gw7] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] [gw11] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] [gw5] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] [gw10] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] [gw6] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] [gw7] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] [gw11] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] [gw9] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] [gw3] [ 36%] PASSED tests/test_binary.py::test_nearest[upstream-True-same] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw10] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] [gw6] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] [gw11] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] [gw7] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] [gw5] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] [gw9] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] [gw11] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] [gw6] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] [gw7] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] [gw10] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] [gw5] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] [gw11] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] [gw6] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] [gw7] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] [gw10] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] [gw5] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] [gw9] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] [gw7] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] [gw6] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] [gw11] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] [gw10] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] [gw5] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] [gw7] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] [gw9] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] [gw11] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] [gw6] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] [gw10] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] [gw5] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] [gw0] [ 42%] PASSED tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_set_union[same] [gw7] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] [gw5] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] [gw10] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] [gw6] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] [gw11] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw7] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] [gw9] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] [gw10] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] [gw11] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] [gw6] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] [gw5] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] [gw7] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] [gw6] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] [gw10] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] [gw1] [ 45%] PASSED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw9] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] [gw2] [ 45%] PASSED tests/test_binary.py::test_coverage[opposite] tests/test_binary.py::test_subtraction[same] [gw7] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] [gw5] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] [gw10] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] [gw6] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] [gw11] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] [gw7] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] [gw9] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] [gw6] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] [gw10] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] [gw7] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] [gw3] [ 47%] PASSED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw5] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] [gw9] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] [gw6] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] [gw10] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] [gw11] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] [gw7] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] [gw9] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] [gw6] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] [gw10] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] [gw7] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] [gw5] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] [gw11] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] [gw6] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] [gw10] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] [gw7] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] [gw9] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] [gw11] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] [gw10] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] [gw7] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] [gw5] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] [gw9] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] [gw6] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] [gw7] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] [gw8] [ 51%] PASSED tests/test_binary.py::test_k_nearest[None-True-opposite-last] tests/test_binary.py::test_k_nearest[None-True-same-last] [gw10] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] [gw11] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] [gw4] [ 52%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw6] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] [gw9] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] [gw5] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] [gw7] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] [gw10] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] [gw6] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw9] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] [gw7] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] [gw11] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] [gw10] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] [gw6] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw5] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] [gw9] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] [gw7] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] [gw10] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] [gw6] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw0] [ 55%] PASSED tests/test_binary.py::test_set_union[same] tests/test_binary.py::test_overlap[False] [gw5] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] [gw11] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] [gw1] [ 56%] PASSED tests/test_binary.py::test_join[False] tests/test_binary.py::test_join[same] [gw7] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] [gw10] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] [gw9] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] [gw6] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] [gw11] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] [gw7] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] [gw5] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] [gw6] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] [gw7] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] [gw9] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] [gw11] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] [gw10] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] [gw6] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] [gw5] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] [gw7] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw9] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] [gw6] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] [gw10] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] [gw3] [ 59%] PASSED tests/test_binary.py::test_nearest[upstream-False-False] tests/test_binary.py::test_nearest[upstream-False-same] [gw7] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw11] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] [gw5] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] [gw6] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] [gw10] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw7] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] [gw9] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] [gw5] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] [gw11] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] [gw6] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] [gw2] [ 61%] PASSED tests/test_binary.py::test_subtraction[same] tests/test_binary.py::test_subtraction[opposite] [gw10] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] [gw7] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] [gw5] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] [gw6] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] [gw9] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] [gw11] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] [gw10] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] [gw7] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] [gw5] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] [gw9] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] [gw6] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] [gw10] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] [gw11] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] [gw7] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] [gw0] [ 64%] PASSED tests/test_binary.py::test_overlap[False] tests/test_binary.py::test_overlap[same] [gw5] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] [gw6] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] [gw9] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] [gw4] [ 65%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] tests/test_binary.py::test_k_nearest[upstream-False-same-last] [gw5] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] [gw10] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw7] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] [gw9] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] [gw11] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] [gw6] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] [gw1] [ 66%] PASSED tests/test_binary.py::test_join[same] tests/test_binary.py::test_join[opposite] [gw10] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] [gw7] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] [gw5] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] [gw9] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] [gw11] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] [gw10] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] [gw7] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] [gw6] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] [gw9] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] [gw10] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] [gw5] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] [gw7] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] [gw6] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] [gw11] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] [gw5] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] [gw10] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] [gw9] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] [gw7] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] [gw6] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] [gw3] [ 70%] PASSED tests/test_binary.py::test_nearest[upstream-False-same] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw11] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] [gw10] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] [gw9] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] [gw5] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] [gw7] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] [gw6] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] [gw11] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] [gw10] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] [gw5] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] [gw7] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] [gw11] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] [gw9] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] [gw6] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] [gw10] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] [gw0] [ 73%] PASSED tests/test_binary.py::test_overlap[same] tests/test_binary.py::test_overlap[opposite] [gw7] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] [gw9] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] [gw6] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] [gw5] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] [gw11] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] [gw10] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] [gw9] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw7] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] [gw6] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] [gw1] [ 75%] PASSED tests/test_binary.py::test_join[opposite] tests/test_binary.py::test_reldist [gw11] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] [gw5] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] [gw10] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] [gw9] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] [gw7] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] [gw11] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] [gw5] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] [gw6] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] [gw11] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] [gw10] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] [gw9] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] [gw7] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] [gw5] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] [gw8] [ 77%] PASSED tests/test_binary.py::test_k_nearest[None-True-same-last] [gw2] [ 78%] PASSED tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_k_nearest[None-True-False-last] [gw11] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] [gw6] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] [gw5] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] [gw4] [ 78%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw7] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] [gw10] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] [gw9] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] [gw6] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] [gw11] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] [gw5] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] [gw10] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] [gw6] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] [gw7] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] [gw9] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] [gw3] [ 80%] PASSED tests/test_binary.py::test_nearest[upstream-False-opposite] tests/test_binary.py::test_nearest[downstream-True-False] [gw5] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] [gw6] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] [gw0] [ 81%] PASSED tests/test_binary.py::test_overlap[opposite] tests/test_binary.py::test_intersect[False] [gw11] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] [gw9] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] [gw10] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] [gw7] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] [gw5] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] [gw6] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] [gw11] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] [gw9] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] [gw7] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] [gw1] [ 83%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw10] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] [gw5] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] [gw6] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] [gw9] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] [gw11] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] [gw10] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] [gw7] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] [gw5] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] [gw6] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] [gw9] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] [gw11] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] [gw10] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] [gw7] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] [gw6] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] [gw5] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] [gw11] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] [gw9] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] [gw7] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] [gw10] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] [gw6] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw9] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] [gw11] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] [gw5] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] [gw10] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] [gw7] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] [gw9] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] [gw11] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] tests/test_genomicfeatures.py::test_introns_single [gw5] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] tests/test_getset_attr.py::test_getsetattr [gw5] [ 88%] PASSED tests/test_getset_attr.py::test_getsetattr tests/test_io.py::test_read_bed [gw5] [ 89%] PASSED tests/test_io.py::test_read_bed tests/test_pickle.py::test_pickle [gw5] [ 89%] PASSED tests/test_pickle.py::test_pickle tests/test_stranded.py::test_stranded [gw6] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw5] [ 89%] PASSED tests/test_stranded.py::test_stranded tests/test_stranded.py::test_unstrand tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] [gw5] [ 89%] PASSED tests/test_stranded.py::test_unstrand tests/test_unary.py::test_merge[True] [gw10] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] tests/test_getset_attr.py::test_getsetattr_fails [gw10] [ 90%] PASSED tests/test_getset_attr.py::test_getsetattr_fails tests/test_unary.py::test_cluster[False] [gw7] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] tests/test_getset_attr.py::test_getsetattr_with_str [gw7] [ 90%] PASSED tests/test_getset_attr.py::test_getsetattr_with_str tests/test_unary.py::test_cluster_by[False] [gw9] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] tests/test_io.py::test_read_gtf [gw9] [ 90%] PASSED tests/test_io.py::test_read_gtf tests/test_unary.py::test_merge_by[False] [gw11] [ 91%] PASSED tests/test_genomicfeatures.py::test_introns_single tests/test_io.py::test_read_gff3 [gw11] [ 91%] PASSED tests/test_io.py::test_read_gff3 tests/test_unary.py::test_init[True] [gw6] [ 91%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] tests/test_unary.py::test_merge[False] [gw0] [ 91%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_intersect[same] [gw2] [ 91%] PASSED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw11] [ 92%] PASSED tests/test_unary.py::test_init[True] tests/test_unary.py::test_init[False] [gw4] [ 92%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-False-last] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw3] [ 92%] PASSED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_binary.py::test_nearest[downstream-True-same] [gw11] [ 92%] PASSED tests/test_unary.py::test_init[False] tests/test_unary.py::test_summary [gw1] [ 92%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw5] [ 93%] PASSED tests/test_unary.py::test_merge[True] tests/test_unary.py::test_cluster[True] [gw6] [ 93%] PASSED tests/test_unary.py::test_merge[False] tests/test_unary.py::test_getitem [gw0] [ 93%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw9] [ 93%] PASSED tests/test_unary.py::test_merge_by[False] tests/test_unary.py::test_windows [gw11] [ 93%] PASSED tests/test_unary.py::test_summary tests/windows/test_windows.py::test_windows [gw11] [ 93%] PASSED tests/windows/test_windows.py::test_windows [gw6] [ 94%] PASSED tests/test_unary.py::test_getitem [gw10] [ 94%] PASSED tests/test_unary.py::test_cluster[False] tests/test_unary.py::test_cluster_by[True] [gw2] [ 94%] PASSED tests/test_binary.py::test_nearest[None-True-False] tests/test_binary.py::test_nearest[None-True-same] [gw3] [ 94%] PASSED tests/test_binary.py::test_nearest[downstream-True-same] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw8] [ 94%] PASSED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw4] [ 95%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_binary.py::test_k_nearest[upstream-True-same-last] [gw0] [ 95%] PASSED tests/test_binary.py::test_intersect[opposite] [gw1] [ 95%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw5] [ 95%] PASSED tests/test_unary.py::test_cluster[True] tests/windows/test_windows.py::test_windows2 [gw5] [ 95%] PASSED tests/windows/test_windows.py::test_windows2 [gw7] [ 96%] PASSED tests/test_unary.py::test_cluster_by[False] tests/test_unary.py::test_merge_by[True] [gw9] [ 96%] PASSED tests/test_unary.py::test_windows [gw3] [ 96%] PASSED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw2] [ 96%] PASSED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw4] [ 96%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw1] [ 96%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-False-last] [gw10] [ 97%] PASSED tests/test_unary.py::test_cluster_by[True] [gw3] [ 97%] PASSED tests/test_binary.py::test_nearest[downstream-False-False] [gw8] [ 97%] PASSED tests/test_binary.py::test_k_nearest_1_vs_nearest tests/test_change_chromosome_custom.py::test_change_chromosomes [gw8] [ 97%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw8] [ 97%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw8] [ 98%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_concat.py::test_concat_unstranded_stranded [gw8] [ 98%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw7] [ 98%] PASSED tests/test_unary.py::test_merge_by[True] [gw8] [ 98%] PASSED tests/test_count_overlaps.py::test_strand_vs_strand_same tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw2] [ 98%] PASSED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw8] [ 99%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw4] [ 99%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw2] [ 99%] PASSED tests/test_binary.py::test_nearest[None-False-False] tests/test_binary.py::test_nearest[None-False-same] [gw2] [ 99%] PASSED tests/test_binary.py::test_nearest[None-False-same] [gw4] [ 99%] PASSED tests/test_binary.py::test_k_nearest[None-False-opposite-last] tests/test_binary.py::test_k_nearest[None-False-same-last] [gw4] [100%] PASSED tests/test_binary.py::test_k_nearest[None-False-same-last] =================================== FAILURES =================================== ____________________ test_k_nearest[None-False-False-last] _____________________ [gw8] linux -- Python 3.12.6 /usr/bin/python3.12 nearest_how = None, overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:559: in test_k_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) tests/helpers.py:58: in assert_df_equal print("index equal", df1.index == df2.index) /usr/lib/python3/dist-packages/pandas/core/ops/common.py:76: in new_method return method(self, other) /usr/lib/python3/dist-packages/pandas/core/arraylike.py:40: in __eq__ return self._cmp_method(other, operator.eq) /usr/lib/python3/dist-packages/pandas/core/indexes/range.py:1070: in _cmp_method return super()._cmp_method(other, op) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = RangeIndex(start=0, stop=6, step=1) other = RangeIndex(start=0, stop=5, step=1), op = def _cmp_method(self, other, op): """ Wrapper used to dispatch comparison operations. """ if self.is_(other): # fastpath if op in {operator.eq, operator.le, operator.ge}: arr = np.ones(len(self), dtype=bool) if self._can_hold_na and not isinstance(self, ABCMultiIndex): # TODO: should set MultiIndex._can_hold_na = False? arr[self.isna()] = False return arr elif op is operator.ne: arr = np.zeros(len(self), dtype=bool) if self._can_hold_na and not isinstance(self, ABCMultiIndex): arr[self.isna()] = True return arr if isinstance(other, (np.ndarray, Index, ABCSeries, ExtensionArray)) and len( self ) != len(other): > raise ValueError("Lengths must match to compare") E ValueError: Lengths must match to compare E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=False, E strandedness=False, E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3 | 4 | a | 0 | - | E | chr1 | 3 | 4 | a | 0 | - | E | chr1 | 3 | 6 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7 | 8 | a | 0 | + | E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7182 E /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7184 E /usr/lib/python3/dist-packages/pandas/core/indexes/range.py:1070 E E You can reproduce this example by temporarily adding @reproduce_failure('6.112.0', b'AXicHYexDQAgEAIPjSaWDuYsFk5s4R7+A4EDAVMLpH3eDYYpbgWKh+Qw1EjFqSb0LPi7/AM7') as a decorator on your test case /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7185: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpijng2oja/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijng2oja/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphpts8ury/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphpts8ury/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvt68isgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvt68isgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 2 chr1 2567198 2568737 - 184524 3 chr1 2567198 2568737 - 246165 4 chr1 2935424 2945424 + 115019 5 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 470969 | 477279 | a | 0 | ... | | chr1 | 470969 | 477279 | a | 0 | ... | | chr1 | 2935424 | 2945424 | a | 0 | ... | | chr1 | 2935424 | 2945424 | a | 0 | ... | | chr1 | 2567198 | 2568737 | a | 0 | ... | | chr1 | 2567198 | 2568737 | a | 0 | ... | | chr1 | 9646164 | 9653887 | a | 0 | ... | | chr1 | 9646164 | 9653887 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 4 chr1 2567198 2568737 - 184524 5 chr1 2567198 2568737 - 246165 2 chr1 2935424 2945424 + 115019 3 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 df2 Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 2 chr1 2567198 2568737 - 184524 3 chr1 2567198 2568737 - 246165 4 chr1 2935424 2945424 + 115019 5 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 Actual Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 2 chr1 2567198 2568737 - 184524 3 chr1 2567198 2568737 - 246165 4 chr1 2935424 2945424 + 115019 5 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 Expected Chromosome Start End Strand Distance 0 chr1 470969 477279 + 1901823 1 chr1 470969 477279 + 2337623 2 chr1 2567198 2568737 - 184524 3 chr1 2567198 2568737 - 246165 4 chr1 2935424 2945424 + 115019 5 chr1 2935424 2945424 + 552750 6 chr1 9646164 9653887 - 6825759 7 chr1 9646164 9653887 - 7263490 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphq17iyon/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphq17iyon/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmz7srey0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmz7srey0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1r5t2qxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1r5t2qxr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpma61y7w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma61y7w9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5526623 | 5530029 | a | 0 | ... | | chr1 | 5526623 | 5530029 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 df2 Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 Actual Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 Expected Chromosome Start End Strand Distance 0 chr1 5526623 5530029 - 2803395 1 chr1 5526623 5530029 - 3433341 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy2uym41w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy2uym41w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_gcd7zwf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gcd7zwf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpykpw_59h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpykpw_59h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv595rge9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv595rge9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7a9rv3r4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7a9rv3r4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqm4gb4hz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqm4gb4hz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2888059 | a | 0 | ... | | chr1 | 2878713 | 2888059 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd45kslz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd45kslz1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2888059 | a | 0 | ... | | chr1 | 2878713 | 2888059 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2888059 + 2807544 1 chr1 2878713 2888059 + 2813173 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq702mrgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq702mrgg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2878714 | a | 0 | ... | | chr1 | 2878713 | 2878714 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2807544 1 chr1 2878713 2878714 + 2813173 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpopvy9kr6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpopvy9kr6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2878714 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2878714 + 2813176 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6rr3g079/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6rr3g079/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2878713 | 2878714 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 df2 Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 Actual Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 Expected Chromosome Start End Strand Distance 0 chr1 2878713 2878714 - 2813176 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpumjx0qw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumjx0qw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw6g_fr5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw6g_fr5v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 2 chr1 5087609 5092865 - 184783 3 chr1 5087609 5092865 - 826946 4 chr1 6158835 6164150 - 231765 5 chr1 6158835 6164150 - 877248 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5087609 | 5087764 | a | 0 | ... | | chr1 | 5087609 | 5087764 | a | 0 | ... | | chr1 | 6158835 | 6164150 | a | 0 | ... | | chr1 | 6158835 | 6164150 | a | 0 | ... | | chr1 | 5087609 | 5092865 | a | 0 | ... | | chr1 | 5087609 | 5092865 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 4 chr1 5087609 5092865 - 184783 5 chr1 5087609 5092865 - 826946 2 chr1 6158835 6164150 - 231765 3 chr1 6158835 6164150 - 877248 df2 Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 2 chr1 5087609 5092865 - 184783 3 chr1 5087609 5092865 - 826946 4 chr1 6158835 6164150 - 231765 5 chr1 6158835 6164150 - 877248 Actual Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 2 chr1 5087609 5092865 - 184783 3 chr1 5087609 5092865 - 826946 4 chr1 6158835 6164150 - 231765 5 chr1 6158835 6164150 - 877248 Expected Chromosome Start End Strand Distance 0 chr1 5087609 5087764 + 189884 1 chr1 5087609 5087764 + 832047 2 chr1 5087609 5092865 - 184783 3 chr1 5087609 5092865 - 826946 4 chr1 6158835 6164150 - 231765 5 chr1 6158835 6164150 - 877248 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmjej5byd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmjej5byd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppu4kf2kt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppu4kf2kt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6pn7z5am/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6pn7z5am/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5eu755ak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5eu755ak/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt6ccla5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6ccla5l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9hty0375/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hty0375/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpteehec2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpteehec2a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_gur1_gr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_gur1_gr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx0neicsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx0neicsr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7308093 | 7314471 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 df2 Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Actual Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Expected Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp05zya_jc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05zya_jc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7308093 | 7314471 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 df2 Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Actual Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Expected Chromosome Start End Strand Distance 0 chr1 7308093 7314471 + 6650683 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2g8lt36f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2g8lt36f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9903 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 df2 Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 Actual Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 Expected Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6nwodw6v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6nwodw6v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 4 chr9 3128776 3131715 + 612750 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9903 | a | 0 | ... | | chr9 | 3128776 | 3131715 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 1 chr9 3128776 3131715 + 612750 df2 Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 4 chr9 3128776 3131715 + 612750 Actual Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 1 chr9 3128776 3131715 + 612750 Expected Chromosome Start End Strand Distance 0 chr1 2 9903 + 643530 1 chr9 3128776 3131715 + 612750 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpls12768j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpls12768j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 4 chr9 9236 9237 + 3735228 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 9902 | a | 0 | ... | | chr9 | 9236 | 9237 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 1 chr9 9236 9237 + 3735228 df2 Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 4 chr9 9236 9237 + 3735228 Actual Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 1 chr9 9236 9237 + 3735228 Expected Chromosome Start End Strand Distance 0 chr1 1 9902 + 643531 1 chr9 9236 9237 + 3735228 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4xclw7uz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xclw7uz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1dfkyxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1dfkyxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp30sua0m1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp30sua0m1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiicjzclu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiicjzclu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpohf2itz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohf2itz6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_t_5f1af/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_t_5f1af/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpww3rh6e4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpww3rh6e4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzxr9_jqi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxr9_jqi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqxycckhv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqxycckhv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtxnb2c5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtxnb2c5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbc0gqz5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc0gqz5v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpltjpy14m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpltjpy14m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb20qmbva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb20qmbva/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9564930 | 9565690 | a | 0 | ... | | chr1 | 3756769 | 3758615 | a | 0 | ... | | chr1 | 5631250 | 5633096 | a | 0 | ... | | chr1 | 6631754 | 6633600 | a | 0 | ... | | chr1 | 3893027 | 3894873 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3756769 3758615 + 6191337 4 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 0 chr1 9564930 9565690 + 384262 df2 Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Actual Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Expected Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa9uy_kba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9uy_kba/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9564930 | 9565690 | a | 0 | ... | | chr1 | 3756769 | 3758615 | a | 0 | ... | | chr1 | 5631250 | 5633096 | a | 0 | ... | | chr1 | 6631754 | 6633600 | a | 0 | ... | | chr1 | 3893027 | 3894873 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3756769 3758615 + 6191337 4 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 0 chr1 9564930 9565690 + 384262 df2 Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Actual Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Expected Chromosome Start End Strand Distance 0 chr1 3756769 3758615 + 6191337 1 chr1 3893027 3894873 + 6055079 2 chr1 5631250 5633096 + 4316856 3 chr1 6631754 6633600 + 3316352 4 chr1 9564930 9565690 + 384262 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_g5vqum0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g5vqum0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2b4gvcw6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2b4gvcw6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnogqcm81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnogqcm81/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3wiry99d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3wiry99d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp47mlkkwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47mlkkwh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppfyli0wh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfyli0wh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2er6p2xz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2er6p2xz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph2cv5jro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2cv5jro/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdcuio71z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcuio71z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf9y_0_3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9y_0_3p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8zln4j0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8zln4j0u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2uwq50zy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uwq50zy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpea9k0skl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea9k0skl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa09g_5tr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa09g_5tr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmxrva_1q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxrva_1q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 1694330 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsshayx4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsshayx4a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr3_y167c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3_y167c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprabamv9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprabamv9n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6529846 | 6532809 | a | 0 | ... | | chr1 | 6529846 | 6532809 | a | 0 | ... | | chr1 | 7309406 | 7311515 | a | 0 | ... | | chr1 | 7309406 | 7311515 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 df2 Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 Actual Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 Expected Chromosome Start End Strand Distance 0 chr1 6529846 6532809 + 152917 1 chr1 6529846 6532809 + 2142343 2 chr1 7309406 7311515 - 932477 3 chr1 7309406 7311515 - 1974698 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfwicx8xf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfwicx8xf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 2 chr1 2292934 2294596 + 14750 3 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 6 chr1 2309345 2316283 - 9899 7 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 12 chr1 9286212 9294610 + 2909283 13 chr1 9286212 9294610 + 4898709 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 6 chr1 2292934 2294596 + 14750 7 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 12 chr1 2309345 2316283 - 9899 13 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 2 chr1 9286212 9294610 + 2909283 3 chr1 9286212 9294610 + 4898709 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 2 chr1 2292934 2294596 + 14750 3 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 6 chr1 2309345 2316283 - 9899 7 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 12 chr1 9286212 9294610 + 2909283 13 chr1 9286212 9294610 + 4898709 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 2 chr1 2292934 2294596 + 14750 3 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 6 chr1 2309345 2316283 - 9899 7 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 12 chr1 9286212 9294610 + 2909283 13 chr1 9286212 9294610 + 4898709 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1212437 1 chr1 1076210 1080498 + 1228848 2 chr1 2292934 2294596 + 14750 3 chr1 2292934 2294596 + 1212437 4 chr1 2292934 2299447 + 9899 5 chr1 2292934 2299447 + 1212437 6 chr1 2309345 2316283 - 9899 7 chr1 2309345 2316283 - 14750 8 chr1 4381762 4387504 - 1984521 9 chr1 4381762 4387504 - 2065480 10 chr1 6372024 6376930 - 1984521 11 chr1 6372024 6376930 - 2909283 12 chr1 9286212 9294610 + 2909283 13 chr1 9286212 9294610 + 4898709 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2yiyuej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2yiyuej/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 2292934 | 2299447 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr3 | 6851060 | 6853898 | a | 0 | ... | | chr5 | 2751097 | 2751853 | a | 0 | ... | | chr6 | 2292934 | 2297051 | a | 0 | ... | | chr20 | 8824422 | 8832590 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 5 chr1 2292934 2294596 + 1207768 6 chr1 2292934 2294596 + 1216717 15 chr6 2292934 2297051 + 1207768 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 11 chr1 2309345 2316283 - 1224179 12 chr1 2309345 2316283 - 1233128 14 chr5 2751097 2751853 - 1674887 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 13 chr3 6851060 6853898 - 6785523 16 chr20 8824422 8832590 + 8758881 1 chr1 9286212 9294610 + 8201046 2 chr1 9286212 9294610 + 8209995 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 16 chr6 2292934 2297051 + 1207768 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 15 chr5 2751097 2751853 - 1674887 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 14 chr3 6851060 6853898 - 6785523 13 chr20 8824422 8832590 + 8758881 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkvleh0l3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkvleh0l3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 2292934 | 2299447 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr3 | 6851060 | 6853898 | a | 0 | ... | | chr5 | 2751097 | 2751853 | a | 0 | ... | | chr6 | 2292934 | 2297051 | a | 0 | ... | | chr20 | 8824422 | 8832590 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 5 chr1 2292934 2294596 + 1207768 6 chr1 2292934 2294596 + 1216717 15 chr6 2292934 2297051 + 1207768 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 11 chr1 2309345 2316283 - 1224179 12 chr1 2309345 2316283 - 1233128 14 chr5 2751097 2751853 - 1674887 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 13 chr3 6851060 6853898 - 6785523 16 chr20 8824422 8832590 + 8758881 1 chr1 9286212 9294610 + 8201046 2 chr1 9286212 9294610 + 8209995 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 16 chr6 2292934 2297051 + 1207768 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 15 chr5 2751097 2751853 - 1674887 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 14 chr3 6851060 6853898 - 6785523 13 chr20 8824422 8832590 + 8758881 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1001653 1 chr1 2292934 2294596 + 1207768 2 chr1 2292934 2294596 + 1216717 3 chr1 2292934 2299447 + 1207768 4 chr1 2292934 2299447 + 1216717 5 chr1 2309345 2316283 - 1224179 6 chr1 2309345 2316283 - 1233128 7 chr1 4381762 4387504 - 3296596 8 chr1 4381762 4387504 - 3305545 9 chr1 6372024 6376930 - 5286858 10 chr1 6372024 6376930 - 5295807 11 chr1 9286212 9294610 + 8201046 12 chr1 9286212 9294610 + 8209995 13 chr20 8824422 8832590 + 8758881 14 chr3 6851060 6853898 - 6785523 15 chr5 2751097 2751853 - 1674887 16 chr6 2292934 2297051 + 1207768 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphblr3p_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphblr3p_7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 2 chr1 2292934 2294596 + 2227397 3 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 6 chr1 2309345 2316283 - 2243808 7 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 12 chr1 9286212 9294610 + 9220675 13 chr1 9286212 9294610 + 9286193 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 6 chr1 2292934 2294596 + 2227397 7 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 12 chr1 2309345 2316283 - 2243808 13 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 2 chr1 9286212 9294610 + 9220675 3 chr1 9286212 9294610 + 9286193 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 2 chr1 2292934 2294596 + 2227397 3 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 6 chr1 2309345 2316283 - 2243808 7 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 12 chr1 9286212 9294610 + 9220675 13 chr1 9286212 9294610 + 9286193 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 2 chr1 2292934 2294596 + 2227397 3 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 6 chr1 2309345 2316283 - 2243808 7 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 12 chr1 9286212 9294610 + 9220675 13 chr1 9286212 9294610 + 9286193 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010673 1 chr1 1076210 1080498 + 1076191 2 chr1 2292934 2294596 + 2227397 3 chr1 2292934 2294596 + 2292915 4 chr1 2292934 2299447 + 2227397 5 chr1 2292934 2299447 + 2292915 6 chr1 2309345 2316283 - 2243808 7 chr1 2309345 2316283 - 2309326 8 chr1 4381762 4387504 - 4316225 9 chr1 4381762 4387504 - 4381743 10 chr1 6372024 6376930 - 6306487 11 chr1 6372024 6376930 - 6372005 12 chr1 9286212 9294610 + 9220675 13 chr1 9286212 9294610 + 9286193 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp64qe5ca6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64qe5ca6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 2 chr1 2292934 2294596 + 2227379 3 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 6 chr1 2309345 2316283 - 2243790 7 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 12 chr1 9286212 9294610 + 9220657 13 chr1 9286212 9294610 + 9220675 14 chr20 8824422 8832590 + 8758867 15 chr3 6851060 6853898 - 6785505 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 1076210 | 1080498 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | chr1 | 9286212 | 9294610 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 6372024 | 6376930 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | | chr1 | 2309345 | 2316283 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 6 chr1 2292934 2294596 + 2227379 7 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 12 chr1 2309345 2316283 - 2243790 13 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 14 chr3 6851060 6853898 - 6785505 15 chr20 8824422 8832590 + 8758867 2 chr1 9286212 9294610 + 9220657 3 chr1 9286212 9294610 + 9220675 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 2 chr1 2292934 2294596 + 2227379 3 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 6 chr1 2309345 2316283 - 2243790 7 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 15 chr3 6851060 6853898 - 6785505 14 chr20 8824422 8832590 + 8758867 12 chr1 9286212 9294610 + 9220657 13 chr1 9286212 9294610 + 9220675 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 2 chr1 2292934 2294596 + 2227379 3 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 6 chr1 2309345 2316283 - 2243790 7 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 12 chr1 9286212 9294610 + 9220657 13 chr1 9286212 9294610 + 9220675 14 chr20 8824422 8832590 + 8758867 15 chr3 6851060 6853898 - 6785505 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1080498 + 1010655 1 chr1 1076210 1080498 + 1010673 2 chr1 2292934 2294596 + 2227379 3 chr1 2292934 2294596 + 2227397 4 chr1 2292934 2299447 + 2227379 5 chr1 2292934 2299447 + 2227397 6 chr1 2309345 2316283 - 2243790 7 chr1 2309345 2316283 - 2243808 8 chr1 4381762 4387504 - 4316207 9 chr1 4381762 4387504 - 4316225 10 chr1 6372024 6376930 - 6306469 11 chr1 6372024 6376930 - 6306487 12 chr1 9286212 9294610 + 9220657 13 chr1 9286212 9294610 + 9220675 14 chr20 8824422 8832590 + 8758867 15 chr3 6851060 6853898 - 6785505 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgr67are2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgr67are2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 1 chr1 1076210 1076215 + 1076200 2 chr1 1076210 1076215 - 1010673 3 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 6 chr1 1076210 1085167 - 1010673 7 chr1 1076210 1085167 - 1076200 8 chr1 1076210 1085167 - 1010673 9 chr1 1076210 1085167 - 1076200 10 chr1 1076210 1085167 - 1010673 11 chr1 1076210 1085167 - 1076200 12 chr2 1076210 1076215 - 1010673 13 chr2 1076210 1085231 - 1010673 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1076210 | 1076215 | a | 0 | ... | | chr1 | 1076210 | 1076215 | a | 0 | ... | | chr1 | 1076210 | 1085167 | a | 0 | ... | | chr1 | 1076210 | 1085167 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1076210 | 1076215 | a | 0 | ... | | chr1 | 1076210 | 1076215 | a | 0 | ... | | chr1 | 1076210 | 1085167 | a | 0 | ... | | chr1 | 1076210 | 1085167 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 8 chr1 1076210 1076215 - 1010673 12 chr2 1076210 1076215 - 1010673 1 chr1 1076210 1076215 + 1076200 9 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 2 chr1 1076210 1085167 - 1010673 6 chr1 1076210 1085167 - 1010673 10 chr1 1076210 1085167 - 1010673 3 chr1 1076210 1085167 - 1076200 7 chr1 1076210 1085167 - 1076200 11 chr1 1076210 1085167 - 1076200 13 chr2 1076210 1085231 - 1010673 df2 Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 2 chr1 1076210 1076215 - 1010673 12 chr2 1076210 1076215 - 1010673 1 chr1 1076210 1076215 + 1076200 3 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 6 chr1 1076210 1085167 - 1010673 8 chr1 1076210 1085167 - 1010673 10 chr1 1076210 1085167 - 1010673 7 chr1 1076210 1085167 - 1076200 9 chr1 1076210 1085167 - 1076200 11 chr1 1076210 1085167 - 1076200 13 chr2 1076210 1085231 - 1010673 Actual Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 1 chr1 1076210 1076215 + 1076200 2 chr1 1076210 1076215 - 1010673 3 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 6 chr1 1076210 1085167 - 1010673 7 chr1 1076210 1085167 - 1010673 8 chr1 1076210 1085167 - 1010673 9 chr1 1076210 1085167 - 1076200 10 chr1 1076210 1085167 - 1076200 11 chr1 1076210 1085167 - 1076200 12 chr2 1076210 1076215 - 1010673 13 chr2 1076210 1085231 - 1010673 Expected Chromosome Start End Strand Distance 0 chr1 1076210 1076215 + 1010673 1 chr1 1076210 1076215 + 1076200 2 chr1 1076210 1076215 - 1010673 3 chr1 1076210 1076215 - 1076200 4 chr1 1076210 1076218 - 1010673 5 chr1 1076210 1076218 - 1076200 6 chr1 1076210 1085167 - 1010673 7 chr1 1076210 1085167 - 1010673 8 chr1 1076210 1085167 - 1010673 9 chr1 1076210 1085167 - 1076200 10 chr1 1076210 1085167 - 1076200 11 chr1 1076210 1085167 - 1076200 12 chr2 1076210 1076215 - 1010673 13 chr2 1076210 1085231 - 1010673 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnokqbaad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnokqbaad/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 170894 178569 + 1416759 1 chr1 2805781 2814560 + 1209787 2 chr1 2813180 2821374 + 1217186 3 chr1 3891627 3891795 + 2295633 4 chr1 5047825 5057824 + 3451831 5 chr1 8366071 8373036 + 6770077 6 chr1 9011544 9016707 + 7415550 7 chr1 9328478 9334107 + 7732484 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | chr1 | 3891627 | 3891795 | a | 0 | ... | | chr1 | 5047825 | 5057824 | a | 0 | ... | | chr1 | 8366071 | 8373036 | a | 0 | ... | | chr1 | 2805781 | 2814560 | a | 0 | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chr1 170894 178569 + 1416759 5 chr1 2805781 2814560 + 1209787 6 chr1 2813180 2821374 + 1217186 2 chr1 3891627 3891795 + 2295633 3 chr1 5047825 5057824 + 3451831 4 chr1 8366071 8373036 + 6770077 0 chr1 9011544 9016707 + 7415550 1 chr1 9328478 9334107 + 7732484 df2 Chromosome Start End Strand Distance 0 chr1 170894 178569 + 1416759 1 chr1 2805781 2814560 + 1209787 2 chr1 2813180 2821374 + 1217186 3 chr1 3891627 3891795 + 2295633 4 chr1 5047825 5057824 + 3451831 5 chr1 8366071 8373036 + 6770077 6 chr1 9011544 9016707 + 7415550 7 chr1 9328478 9334107 + 7732484 Actual Chromosome Start End Strand Distance 0 chr1 170894 178569 + 1416759 1 chr1 2805781 2814560 + 1209787 2 chr1 2813180 2821374 + 1217186 3 chr1 3891627 3891795 + 2295633 4 chr1 5047825 5057824 + 3451831 5 chr1 8366071 8373036 + 6770077 6 chr1 9011544 9016707 + 7415550 7 chr1 9328478 9334107 + 7732484 Expected Chromosome Start End Strand Distance 0 chr1 170894 178569 + 1416759 1 chr1 2805781 2814560 + 1209787 2 chr1 2813180 2821374 + 1217186 3 chr1 3891627 3891795 + 2295633 4 chr1 5047825 5057824 + 3451831 5 chr1 8366071 8373036 + 6770077 6 chr1 9011544 9016707 + 7415550 7 chr1 9328478 9334107 + 7732484 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9jnnl5q4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jnnl5q4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 311772 15 chr1 9328478 9334107 + 955443 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr1 170894 178569 + 2627213 15 chr1 170894 178569 + 2634612 10 chr1 2805781 2814560 + 1077068 11 chr1 2805781 2814560 + 2233266 12 chr1 2813180 2821374 + 1070254 13 chr1 2813180 2821374 + 2226452 4 chr1 3891627 3891795 + 1070254 5 chr1 3891627 3891795 + 1077068 6 chr1 5047825 5057824 + 1156031 7 chr1 5047825 5057824 + 2226452 8 chr1 8366071 8373036 + 638509 9 chr1 8366071 8373036 + 955443 0 chr1 9011544 9016707 + 311772 1 chr1 9011544 9016707 + 638509 2 chr1 9328478 9334107 + 311772 3 chr1 9328478 9334107 + 955443 df2 Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 311772 15 chr1 9328478 9334107 + 955443 Actual Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 311772 15 chr1 9328478 9334107 + 955443 Expected Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 311772 15 chr1 9328478 9334107 + 955443 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1awll_f6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1awll_f6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 316933 15 chr1 9328478 9334107 + 955443 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9011544 | 9016707 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | chr1 | 9328478 | 9334107 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 2813180 | 2821374 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | | chr1 | 170894 | 178569 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr1 170894 178569 + 2627213 15 chr1 170894 178569 + 2634612 10 chr1 2805781 2814560 + 1077068 11 chr1 2805781 2814560 + 2233266 12 chr1 2813180 2821374 + 1070254 13 chr1 2813180 2821374 + 2226452 4 chr1 3891627 3891795 + 1070254 5 chr1 3891627 3891795 + 1077068 6 chr1 5047825 5057824 + 1156031 7 chr1 5047825 5057824 + 2226452 8 chr1 8366071 8373036 + 638509 9 chr1 8366071 8373036 + 955443 0 chr1 9011544 9016707 + 311772 1 chr1 9011544 9016707 + 638509 2 chr1 9328478 9334107 + 316933 3 chr1 9328478 9334107 + 955443 df2 Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 316933 15 chr1 9328478 9334107 + 955443 Actual Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 316933 15 chr1 9328478 9334107 + 955443 Expected Chromosome Start End Strand Distance 0 chr1 170894 178569 + 2627213 1 chr1 170894 178569 + 2634612 2 chr1 2805781 2814560 + 1077068 3 chr1 2805781 2814560 + 2233266 4 chr1 2813180 2821374 + 1070254 5 chr1 2813180 2821374 + 2226452 6 chr1 3891627 3891795 + 1070254 7 chr1 3891627 3891795 + 1077068 8 chr1 5047825 5057824 + 1156031 9 chr1 5047825 5057824 + 2226452 10 chr1 8366071 8373036 + 638509 11 chr1 8366071 8373036 + 955443 12 chr1 9011544 9016707 + 311772 13 chr1 9011544 9016707 + 638509 14 chr1 9328478 9334107 + 316933 15 chr1 9328478 9334107 + 955443 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplwm47ss3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplwm47ss3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 78 1 chr1 1 2 - 78 2 chr1 1 2 - 78 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpivjvkf3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivjvkf3d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 78 4 chr1 1 2 - 9 5 chr1 1 2 - 78 6 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 8 chr1 1 3673 - 61865 9 chr1 1 5122 - 60416 10 chr1 1 669 - 64869 11 chr1 1 9854 - 55684 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 9854 | a | 0 | ... | | chr1 | 1 | 2435 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 5122 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 669 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 9 5 chr1 1 2 - 9 9 chr1 1 2 - 9 1 chr1 1 2 + 78 6 chr1 1 2 - 78 10 chr1 1 2 - 78 11 chr1 1 669 - 64869 3 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 4 chr1 1 3673 - 61865 8 chr1 1 5122 - 60416 2 chr1 1 9854 - 55684 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 9 2 chr1 1 2 - 9 4 chr1 1 2 - 9 1 chr1 1 2 + 78 3 chr1 1 2 - 78 5 chr1 1 2 - 78 10 chr1 1 669 - 64869 6 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 8 chr1 1 3673 - 61865 9 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 9 4 chr1 1 2 - 78 5 chr1 1 2 - 78 6 chr1 1 669 - 64869 7 chr1 1 2435 - 63103 8 chr1 1 3336 - 62202 9 chr1 1 3673 - 61865 10 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 9 4 chr1 1 2 - 78 5 chr1 1 2 - 78 6 chr1 1 669 - 64869 7 chr1 1 2435 - 63103 8 chr1 1 3336 - 62202 9 chr1 1 3673 - 61865 10 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsbdrzmz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsbdrzmz5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 78 4 chr1 1 2 - 9 5 chr1 1 2 - 78 6 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 8 chr1 1 3673 - 61865 9 chr1 1 5122 - 60416 10 chr1 1 669 - 64869 11 chr1 1 9854 - 55684 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 9854 | a | 0 | ... | | chr1 | 1 | 2435 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 5122 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 669 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 9 5 chr1 1 2 - 9 9 chr1 1 2 - 9 1 chr1 1 2 + 78 6 chr1 1 2 - 78 10 chr1 1 2 - 78 11 chr1 1 669 - 64869 3 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 4 chr1 1 3673 - 61865 8 chr1 1 5122 - 60416 2 chr1 1 9854 - 55684 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 9 2 chr1 1 2 - 9 4 chr1 1 2 - 9 1 chr1 1 2 + 78 3 chr1 1 2 - 78 5 chr1 1 2 - 78 10 chr1 1 669 - 64869 6 chr1 1 2435 - 63103 7 chr1 1 3336 - 62202 8 chr1 1 3673 - 61865 9 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 9 4 chr1 1 2 - 78 5 chr1 1 2 - 78 6 chr1 1 669 - 64869 7 chr1 1 2435 - 63103 8 chr1 1 3336 - 62202 9 chr1 1 3673 - 61865 10 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 9 1 chr1 1 2 + 78 2 chr1 1 2 - 9 3 chr1 1 2 - 9 4 chr1 1 2 - 78 5 chr1 1 2 - 78 6 chr1 1 669 - 64869 7 chr1 1 2435 - 63103 8 chr1 1 3336 - 62202 9 chr1 1 3673 - 61865 10 chr1 1 5122 - 60416 11 chr1 1 9854 - 55684 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmf7ybvgk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmf7ybvgk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 8558 - 56980 1 chr1 10 47 - 33 2 chr1 10 47 - 65491 3 chr1 79 336 - 33 4 chr1 79 336 - 65202 5 chr1 79 336 - 33 6 chr1 79 336 - 65202 7 chr1 79 336 - 33 8 chr1 79 336 - 65202 9 chr1 79 336 - 33 10 chr1 79 336 - 65202 11 chr1 79 85 - 33 12 chr1 79 85 - 65453 13 chr1 65537 65794 - 56980 14 chr1 65537 65794 - 65202 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10 | 47 | a | 0 | ... | | chr1 | 10 | 47 | a | 0 | ... | | chr1 | 1 | 8558 | a | 0 | ... | | chr1 | 79 | 336 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 79 | 336 | a | 0 | ... | | chr1 | 79 | 336 | a | 0 | ... | | chr1 | 79 | 336 | a | 0 | ... | | chr1 | 79 | 336 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 8558 - 56980 0 chr1 10 47 - 33 1 chr1 10 47 - 65491 9 chr1 79 85 - 33 10 chr1 79 85 - 65453 3 chr1 79 336 - 33 7 chr1 79 336 - 33 11 chr1 79 336 - 33 13 chr1 79 336 - 33 4 chr1 79 336 - 65202 8 chr1 79 336 - 65202 12 chr1 79 336 - 65202 14 chr1 79 336 - 65202 5 chr1 65537 65794 - 56980 6 chr1 65537 65794 - 65202 df2 Chromosome Start End Strand Distance 0 chr1 1 8558 - 56980 1 chr1 10 47 - 33 2 chr1 10 47 - 65491 11 chr1 79 85 - 33 12 chr1 79 85 - 65453 3 chr1 79 336 - 33 5 chr1 79 336 - 33 7 chr1 79 336 - 33 9 chr1 79 336 - 33 4 chr1 79 336 - 65202 6 chr1 79 336 - 65202 8 chr1 79 336 - 65202 10 chr1 79 336 - 65202 13 chr1 65537 65794 - 56980 14 chr1 65537 65794 - 65202 Actual Chromosome Start End Strand Distance 0 chr1 1 8558 - 56980 1 chr1 10 47 - 33 2 chr1 10 47 - 65491 3 chr1 79 85 - 33 4 chr1 79 85 - 65453 5 chr1 79 336 - 33 6 chr1 79 336 - 33 7 chr1 79 336 - 33 8 chr1 79 336 - 33 9 chr1 79 336 - 65202 10 chr1 79 336 - 65202 11 chr1 79 336 - 65202 12 chr1 79 336 - 65202 13 chr1 65537 65794 - 56980 14 chr1 65537 65794 - 65202 Expected Chromosome Start End Strand Distance 0 chr1 1 8558 - 56980 1 chr1 10 47 - 33 2 chr1 10 47 - 65491 3 chr1 79 85 - 33 4 chr1 79 85 - 65453 5 chr1 79 336 - 33 6 chr1 79 336 - 33 7 chr1 79 336 - 33 8 chr1 79 336 - 33 9 chr1 79 336 - 65202 10 chr1 79 336 - 65202 11 chr1 79 336 - 65202 12 chr1 79 336 - 65202 13 chr1 65537 65794 - 56980 14 chr1 65537 65794 - 65202 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=15, step=1) index equal [ True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplz14tyeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplz14tyeh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 1860385 1 chr1 4849198 4856651 + 2572220 2 chr1 7826699 7828323 - 1101479 3 chr1 7826699 7828323 - 5549721 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpja764doa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja764doa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 2970049 1 chr1 7826699 7828323 - 2970049 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2je2aeah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2je2aeah/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy7q4rta2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy7q4rta2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821758 1 chr1 7826699 7828323 - 2977500 2 chr1 7826699 7828323 - 6799259 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqd2q9kou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd2q9kou/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd7wn65c2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7wn65c2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4849198 | 4856651 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | | chr1 | 7826699 | 7828323 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 3821759 1 chr1 7826699 7828323 - 2977501 2 chr1 7826699 7828323 - 6799260 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_mgn8bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_mgn8bi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 4783661 1 chr1 7826699 7826700 + 7761162 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7826699 | 7826700 | a | 0 | ... | | chr1 | 4849198 | 4856651 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4849198 4856651 + 4783661 0 chr1 7826699 7826700 + 7761162 df2 Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 4783661 1 chr1 7826699 7826700 + 7761162 Actual Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 4783661 1 chr1 7826699 7826700 + 7761162 Expected Chromosome Start End Strand Distance 0 chr1 4849198 4856651 + 4783661 1 chr1 7826699 7826700 + 7761162 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb1m32uvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1m32uvq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 6 chr12 5191349 5197809 + 4082195 7 chr15 221755 224156 - 86234 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 1550927 | 1560604 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr12 | 5191349 | 5197809 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr15 221755 224156 - 86234 2 chr1 1550927 1560604 - 6265203 5 chr12 5191349 5197809 + 4082195 3 chr1 7078483 7087002 - 738805 4 chr1 7148878 7151354 - 674453 1 chr1 7149314 7153375 - 672432 0 chr1 8264194 8264945 - 434118 df2 Chromosome Start End Strand Distance 7 chr15 221755 224156 - 86234 0 chr1 1550927 1560604 - 6265203 6 chr12 5191349 5197809 + 4082195 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph6_9vnlg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6_9vnlg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 6 chr12 5191349 5197809 + 4082195 7 chr15 221755 224156 - 86234 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 1550927 | 1560604 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr12 | 5191349 | 5197809 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr15 221755 224156 - 86234 2 chr1 1550927 1560604 - 6265203 5 chr12 5191349 5197809 + 4082195 3 chr1 7078483 7087002 - 738805 4 chr1 7148878 7151354 - 674453 1 chr1 7149314 7153375 - 672432 0 chr1 8264194 8264945 - 434118 df2 Chromosome Start End Strand Distance 7 chr15 221755 224156 - 86234 0 chr1 1550927 1560604 - 6265203 6 chr12 5191349 5197809 + 4082195 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkved3xh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkved3xh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 6 chr12 5191349 5197809 + 4082195 7 chr15 221755 224156 - 86234 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 1550927 | 1560604 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr12 | 5191349 | 5197809 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr15 221755 224156 - 86234 2 chr1 1550927 1560604 - 6265203 5 chr12 5191349 5197809 + 4082195 3 chr1 7078483 7087002 - 738805 4 chr1 7148878 7151354 - 674453 1 chr1 7149314 7153375 - 672432 0 chr1 8264194 8264945 - 434118 df2 Chromosome Start End Strand Distance 7 chr15 221755 224156 - 86234 0 chr1 1550927 1560604 - 6265203 6 chr12 5191349 5197809 + 4082195 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 6265203 1 chr1 7078483 7087002 - 738805 2 chr1 7148878 7151354 - 674453 3 chr1 7149314 7153375 - 672432 4 chr1 8264194 8264945 - 434118 5 chr12 5191349 5197809 + 4082195 6 chr15 221755 224156 - 86234 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz85mqga0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz85mqga0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 5517880 1 chr1 1550927 1560604 - 5588275 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 61877 5 chr1 7148878 7151354 - 1112841 6 chr1 7149314 7153375 - 62313 7 chr1 7149314 7153375 - 1110820 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1550927 1560604 - 5517880 5 chr1 1550927 1560604 - 5588275 6 chr1 7078483 7087002 - 61877 7 chr1 7078483 7087002 - 62313 8 chr1 7148878 7151354 - 61877 9 chr1 7148878 7151354 - 1112841 2 chr1 7149314 7153375 - 62313 3 chr1 7149314 7153375 - 1110820 0 chr1 8264194 8264945 - 1110820 1 chr1 8264194 8264945 - 1112841 df2 Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 5517880 1 chr1 1550927 1560604 - 5588275 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 61877 5 chr1 7148878 7151354 - 1112841 6 chr1 7149314 7153375 - 62313 7 chr1 7149314 7153375 - 1110820 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 5517880 1 chr1 1550927 1560604 - 5588275 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 61877 5 chr1 7148878 7151354 - 1112841 6 chr1 7149314 7153375 - 62313 7 chr1 7149314 7153375 - 1110820 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 5517880 1 chr1 1550927 1560604 - 5588275 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 61877 5 chr1 7148878 7151354 - 1112841 6 chr1 7149314 7153375 - 62313 7 chr1 7149314 7153375 - 1110820 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa20em6tr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa20em6tr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1542404 1 chr1 1550927 1560604 - 1550176 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 5588275 5 chr1 7148878 7151354 - 7140355 6 chr1 7149314 7153375 - 5588711 7 chr1 7149314 7153375 - 7140791 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7078483 | 7087002 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | | chr1 | 7148878 | 7151354 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1550927 1560604 - 1542404 5 chr1 1550927 1560604 - 1550176 6 chr1 7078483 7087002 - 61877 7 chr1 7078483 7087002 - 62313 8 chr1 7148878 7151354 - 5588275 9 chr1 7148878 7151354 - 7140355 2 chr1 7149314 7153375 - 5588711 3 chr1 7149314 7153375 - 7140791 0 chr1 8264194 8264945 - 1110820 1 chr1 8264194 8264945 - 1112841 df2 Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1542404 1 chr1 1550927 1560604 - 1550176 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 5588275 5 chr1 7148878 7151354 - 7140355 6 chr1 7149314 7153375 - 5588711 7 chr1 7149314 7153375 - 7140791 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1542404 1 chr1 1550927 1560604 - 1550176 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 5588275 5 chr1 7148878 7151354 - 7140355 6 chr1 7149314 7153375 - 5588711 7 chr1 7149314 7153375 - 7140791 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1542404 1 chr1 1550927 1560604 - 1550176 2 chr1 7078483 7087002 - 61877 3 chr1 7078483 7087002 - 62313 4 chr1 7148878 7151354 - 5588275 5 chr1 7148878 7151354 - 7140355 6 chr1 7149314 7153375 - 5588711 7 chr1 7149314 7153375 - 7140791 8 chr1 8264194 8264945 - 1110820 9 chr1 8264194 8264945 - 1112841 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm8tin5a8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8tin5a8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1531574 1 chr1 1550927 1560604 - 1533890 2 chr1 7078483 7087002 - 7059130 3 chr1 7078483 7087002 - 7061446 4 chr1 7148878 7151354 - 7129525 5 chr1 7148878 7151354 - 7131841 6 chr1 7149314 7153375 - 7129961 7 chr1 7149314 7153375 - 7132277 8 chr1 8264194 8264945 - 8244841 9 chr1 8264194 8264945 - 8247157 10 chr11 7674207 7674929 + 7672764 12 chr15 221755 224156 - 216954 14 chr5 9877776 9883670 - 9865989 15 chrX 6801859 6811661 + 6782256 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr5 | 9877776 | 9883670 | a | 0 | ... | | chr11 | 7674207 | 7674929 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | | chrX | 6801859 | 6811661 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 12 chr15 221755 224156 - 216954 4 chr1 1550927 1560604 - 1531574 5 chr1 1550927 1560604 - 1533890 13 chrX 6801859 6811661 + 6782256 6 chr1 7078483 7087002 - 7059130 7 chr1 7078483 7087002 - 7061446 8 chr1 7148878 7151354 - 7129525 9 chr1 7148878 7151354 - 7131841 2 chr1 7149314 7153375 - 7129961 3 chr1 7149314 7153375 - 7132277 11 chr11 7674207 7674929 + 7672764 0 chr1 8264194 8264945 - 8244841 1 chr1 8264194 8264945 - 8247157 10 chr5 9877776 9883670 - 9865989 df2 Chromosome Start End Strand Distance 12 chr15 221755 224156 - 216954 0 chr1 1550927 1560604 - 1531574 1 chr1 1550927 1560604 - 1533890 15 chrX 6801859 6811661 + 6782256 2 chr1 7078483 7087002 - 7059130 3 chr1 7078483 7087002 - 7061446 4 chr1 7148878 7151354 - 7129525 5 chr1 7148878 7151354 - 7131841 6 chr1 7149314 7153375 - 7129961 7 chr1 7149314 7153375 - 7132277 10 chr11 7674207 7674929 + 7672764 8 chr1 8264194 8264945 - 8244841 9 chr1 8264194 8264945 - 8247157 14 chr5 9877776 9883670 - 9865989 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1531574 1 chr1 1550927 1560604 - 1533890 2 chr1 7078483 7087002 - 7059130 3 chr1 7078483 7087002 - 7061446 4 chr1 7148878 7151354 - 7129525 5 chr1 7148878 7151354 - 7131841 6 chr1 7149314 7153375 - 7129961 7 chr1 7149314 7153375 - 7132277 8 chr1 8264194 8264945 - 8244841 9 chr1 8264194 8264945 - 8247157 10 chr11 7674207 7674929 + 7672764 11 chr15 221755 224156 - 216954 12 chr5 9877776 9883670 - 9865989 13 chrX 6801859 6811661 + 6782256 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1531574 1 chr1 1550927 1560604 - 1533890 2 chr1 7078483 7087002 - 7059130 3 chr1 7078483 7087002 - 7061446 4 chr1 7148878 7151354 - 7129525 5 chr1 7148878 7151354 - 7131841 6 chr1 7149314 7153375 - 7129961 7 chr1 7149314 7153375 - 7132277 8 chr1 8264194 8264945 - 8244841 9 chr1 8264194 8264945 - 8247157 10 chr11 7674207 7674929 + 7672764 11 chr15 221755 224156 - 216954 12 chr5 9877776 9883670 - 9865989 13 chrX 6801859 6811661 + 6782256 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgnut2t7n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnut2t7n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1540500 1 chr1 1550927 1560604 - 1541658 2 chr1 7078483 7087002 - 7068056 3 chr1 7078483 7087002 - 7069214 4 chr1 7148878 7151354 - 7138451 5 chr1 7148878 7151354 - 7139609 6 chr1 7149314 7153375 - 7138887 7 chr1 7149314 7153375 - 7140045 8 chr1 8264194 8264945 - 8253767 9 chr1 8264194 8264945 - 8254925 10 chr11 7674207 7674929 + 7672735 12 chr15 221755 224156 - 218604 13 chr3 1 723 + 29 14 chr5 9877776 9883670 - 9871132 15 chrX 6801859 6811661 + 6791307 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 8264194 | 8264945 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | chr1 | 7149314 | 7153375 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr5 | 9877776 | 9883670 | a | 0 | ... | | chr11 | 7674207 | 7674929 | a | 0 | ... | | chr15 | 221755 | 224156 | a | 0 | ... | | chrX | 6801859 | 6811661 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr3 1 723 + 29 13 chr15 221755 224156 - 218604 4 chr1 1550927 1560604 - 1540500 5 chr1 1550927 1560604 - 1541658 14 chrX 6801859 6811661 + 6791307 6 chr1 7078483 7087002 - 7068056 7 chr1 7078483 7087002 - 7069214 8 chr1 7148878 7151354 - 7138451 9 chr1 7148878 7151354 - 7139609 2 chr1 7149314 7153375 - 7138887 3 chr1 7149314 7153375 - 7140045 12 chr11 7674207 7674929 + 7672735 0 chr1 8264194 8264945 - 8253767 1 chr1 8264194 8264945 - 8254925 11 chr5 9877776 9883670 - 9871132 df2 Chromosome Start End Strand Distance 13 chr3 1 723 + 29 12 chr15 221755 224156 - 218604 0 chr1 1550927 1560604 - 1540500 1 chr1 1550927 1560604 - 1541658 15 chrX 6801859 6811661 + 6791307 2 chr1 7078483 7087002 - 7068056 3 chr1 7078483 7087002 - 7069214 4 chr1 7148878 7151354 - 7138451 5 chr1 7148878 7151354 - 7139609 6 chr1 7149314 7153375 - 7138887 7 chr1 7149314 7153375 - 7140045 10 chr11 7674207 7674929 + 7672735 8 chr1 8264194 8264945 - 8253767 9 chr1 8264194 8264945 - 8254925 14 chr5 9877776 9883670 - 9871132 Actual Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1540500 1 chr1 1550927 1560604 - 1541658 2 chr1 7078483 7087002 - 7068056 3 chr1 7078483 7087002 - 7069214 4 chr1 7148878 7151354 - 7138451 5 chr1 7148878 7151354 - 7139609 6 chr1 7149314 7153375 - 7138887 7 chr1 7149314 7153375 - 7140045 8 chr1 8264194 8264945 - 8253767 9 chr1 8264194 8264945 - 8254925 10 chr11 7674207 7674929 + 7672735 11 chr15 221755 224156 - 218604 12 chr3 1 723 + 29 13 chr5 9877776 9883670 - 9871132 14 chrX 6801859 6811661 + 6791307 Expected Chromosome Start End Strand Distance 0 chr1 1550927 1560604 - 1540500 1 chr1 1550927 1560604 - 1541658 2 chr1 7078483 7087002 - 7068056 3 chr1 7078483 7087002 - 7069214 4 chr1 7148878 7151354 - 7138451 5 chr1 7148878 7151354 - 7139609 6 chr1 7149314 7153375 - 7138887 7 chr1 7149314 7153375 - 7140045 8 chr1 8264194 8264945 - 8253767 9 chr1 8264194 8264945 - 8254925 10 chr11 7674207 7674929 + 7672735 11 chr15 221755 224156 - 218604 12 chr3 1 723 + 29 13 chr5 9877776 9883670 - 9871132 14 chrX 6801859 6811661 + 6791307 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=15, step=1) index equal [ True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6cff2wvn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cff2wvn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4456359 | 4456634 | a | 0 | ... | | chr1 | 8017027 | 8017372 | a | 0 | ... | | chr1 | 7501587 | 7508273 | a | 0 | ... | | chr1 | 10000000 | 10002710 | a | 0 | ... | | chr1 | 10000000 | 10009559 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 2 chr1 7501587 7508273 + 4470141 1 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_97pt58i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_97pt58i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4456359 | 4456634 | a | 0 | ... | | chr1 | 8017027 | 8017372 | a | 0 | ... | | chr1 | 7501587 | 7508273 | a | 0 | ... | | chr1 | 10000000 | 10002710 | a | 0 | ... | | chr1 | 10000000 | 10009559 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 2 chr1 7501587 7508273 + 4470141 1 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456634 + 1424913 1 chr1 7501587 7508273 + 4470141 2 chr1 8017027 8017372 + 4985581 3 chr1 10000000 10002710 - 6968554 4 chr1 10000000 10009559 - 6968554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8jmo_oki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jmo_oki/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390770 1 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 3 chr1 10000000 10000004 - 9934411 4 chr1 10000000 10000257 + 9934411 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 4456359 | 4456363 | a | 0 | ... | | chr1 | 8017027 | 8017028 | a | 0 | ... | | chr1 | 7501587 | 7501591 | a | 0 | ... | | chr1 | 10000000 | 10000004 | a | 0 | ... | | chr2 | 5920462 | 5920466 | a | 0 | ... | | chr2 | 5920462 | 5920466 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4456359 4456363 - 4390770 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 3 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 4 chr1 10000000 10000004 - 9934411 0 chr1 10000000 10000257 + 9934411 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390770 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 1 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 3 chr1 10000000 10000004 - 9934411 4 chr1 10000000 10000257 + 9934411 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390770 1 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 3 chr1 10000000 10000004 - 9934411 4 chr1 10000000 10000257 + 9934411 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390770 1 chr1 7501587 7501591 - 7435998 2 chr1 8017027 8017028 - 7951438 3 chr1 10000000 10000004 - 9934411 4 chr1 10000000 10000257 + 9934411 5 chr2 5920462 5920466 + 855992 6 chr2 5920462 5920466 + 5854669 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzk81v9o9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzk81v9o9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390822 1 chr1 4456359 4456363 - 4456357 2 chr1 7501587 7501591 - 7436050 3 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 6 chr1 10000000 10000004 - 9934463 7 chr1 10000000 10000004 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 4456359 | 4456363 | a | 0 | ... | | chr1 | 4456359 | 4456363 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7501587 | 7501591 | a | 0 | ... | | chr1 | 7501587 | 7501591 | a | 0 | ... | | chr1 | 10000000 | 10000004 | a | 0 | ... | | chr1 | 10000000 | 10000004 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 4456359 4456363 - 4390822 3 chr1 4456359 4456363 - 4456357 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 6 chr1 7501587 7501591 - 7436050 7 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 8 chr1 10000000 10000004 - 9934463 9 chr1 10000000 10000004 - 9999998 0 chr1 10000000 10000257 + 9934463 1 chr1 10000000 10000257 + 9999998 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390822 1 chr1 4456359 4456363 - 4456357 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 2 chr1 7501587 7501591 - 7436050 3 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 6 chr1 10000000 10000004 - 9934463 7 chr1 10000000 10000004 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390822 1 chr1 4456359 4456363 - 4456357 2 chr1 7501587 7501591 - 7436050 3 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 6 chr1 10000000 10000004 - 9934463 7 chr1 10000000 10000004 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456363 - 4390822 1 chr1 4456359 4456363 - 4456357 2 chr1 7501587 7501591 - 7436050 3 chr1 7501587 7501591 - 7501585 4 chr1 8017027 8017028 - 7951490 5 chr1 8017027 8017028 - 8017025 6 chr1 10000000 10000004 - 9934463 7 chr1 10000000 10000004 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920466 + 855992 11 chr2 5920462 5920466 + 5854925 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjzm3hvf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzm3hvf7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 4456359 4456616 - 4456357 2 chr1 7501587 7501589 - 7436050 3 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 6 chr1 10000000 10000002 - 9934463 7 chr1 10000000 10000002 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 4456359 | 4456616 | a | 0 | ... | | chr1 | 4456359 | 4456616 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7501587 | 7501589 | a | 0 | ... | | chr1 | 7501587 | 7501589 | a | 0 | ... | | chr1 | 10000000 | 10000002 | a | 0 | ... | | chr1 | 10000000 | 10000002 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 4456359 4456616 - 4390822 3 chr1 4456359 4456616 - 4456357 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 6 chr1 7501587 7501589 - 7436050 7 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 8 chr1 10000000 10000002 - 9934463 9 chr1 10000000 10000002 - 9999998 0 chr1 10000000 10000257 + 9934463 1 chr1 10000000 10000257 + 9999998 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 4456359 4456616 - 4456357 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 2 chr1 7501587 7501589 - 7436050 3 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 6 chr1 10000000 10000002 - 9934463 7 chr1 10000000 10000002 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 4456359 4456616 - 4456357 2 chr1 7501587 7501589 - 7436050 3 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 6 chr1 10000000 10000002 - 9934463 7 chr1 10000000 10000002 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 4456359 4456616 - 4456357 2 chr1 7501587 7501589 - 7436050 3 chr1 7501587 7501589 - 7501585 4 chr1 8017027 8019076 - 7951490 5 chr1 8017027 8019076 - 8017025 6 chr1 10000000 10000002 - 9934463 7 chr1 10000000 10000002 - 9999998 8 chr1 10000000 10000257 + 9934463 9 chr1 10000000 10000257 + 9999998 10 chr2 5920462 5920464 + 855994 11 chr2 5920462 5920464 + 5854925 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2tlmyeo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2tlmyeo0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 7501587 7501589 - 7436050 2 chr1 8017027 8019076 + 7951490 3 chr1 10000000 10000002 - 9934463 4 chr1 10000000 10000257 - 9934463 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8017027 | 8019076 | a | 0 | ... | | chr1 | 4456359 | 4456616 | a | 0 | ... | | chr1 | 10000000 | 10000257 | a | 0 | ... | | chr1 | 7501587 | 7501589 | a | 0 | ... | | chr1 | 10000000 | 10000002 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4456359 4456616 - 4390822 3 chr1 7501587 7501589 - 7436050 0 chr1 8017027 8019076 + 7951490 4 chr1 10000000 10000002 - 9934463 2 chr1 10000000 10000257 - 9934463 df2 Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 7501587 7501589 - 7436050 2 chr1 8017027 8019076 + 7951490 3 chr1 10000000 10000002 - 9934463 4 chr1 10000000 10000257 - 9934463 Actual Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 7501587 7501589 - 7436050 2 chr1 8017027 8019076 + 7951490 3 chr1 10000000 10000002 - 9934463 4 chr1 10000000 10000257 - 9934463 Expected Chromosome Start End Strand Distance 0 chr1 4456359 4456616 - 4390822 1 chr1 7501587 7501589 - 7436050 2 chr1 8017027 8019076 + 7951490 3 chr1 10000000 10000002 - 9934463 4 chr1 10000000 10000257 - 9934463 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgqsyuxjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqsyuxjg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 919564 | 921707 | a | 0 | ... | | chr1 | 919564 | 921707 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 df2 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Expected Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9di_9tes/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9di_9tes/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 919564 | 921707 | a | 0 | ... | | chr1 | 919564 | 921707 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 df2 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Expected Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd3smunqk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3smunqk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 919564 | 921707 | a | 0 | ... | | chr1 | 919564 | 921707 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 df2 Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Expected Chromosome Start End Strand Distance 0 chr1 919564 921707 + 1310562 1 chr1 919564 921707 + 3798949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvgu35mrh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvgu35mrh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2232268 | 2232269 | a | 0 | ... | | chr1 | 4720655 | 4720656 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 df2 Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 Actual Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 Expected Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2488387 1 chr1 4720655 4720656 + 2488387 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpttmrajd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttmrajd2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2232268 | 2232269 | a | 0 | ... | | chr1 | 4720655 | 4720656 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 df2 Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 Actual Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 Expected Chromosome Start End Strand Distance 0 chr1 2232268 2232269 + 2166731 1 chr1 4720655 4720656 + 4655118 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp35rxp6q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp35rxp6q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 797760 | 804742 | a | 0 | ... | | chr1 | 5349582 | 5351801 | a | 0 | ... | | chr1 | 5971841 | 5981508 | a | 0 | ... | | chr1 | 341319 | 343309 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 341319 343309 + 2164325 0 chr1 797760 804742 + 1702892 1 chr1 5349582 5351801 + 2839053 2 chr1 5971841 5981508 + 3461312 df2 Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Actual Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Expected Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvqyj0x8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvqyj0x8n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 797760 | 804742 | a | 0 | ... | | chr1 | 5349582 | 5351801 | a | 0 | ... | | chr1 | 5971841 | 5981508 | a | 0 | ... | | chr1 | 341319 | 343309 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 341319 343309 + 2164325 0 chr1 797760 804742 + 1702892 1 chr1 5349582 5351801 + 2839053 2 chr1 5971841 5981508 + 3461312 df2 Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Actual Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Expected Chromosome Start End Strand Distance 0 chr1 341319 343309 + 2164325 1 chr1 797760 804742 + 1702892 2 chr1 5349582 5351801 + 2839053 3 chr1 5971841 5981508 + 3461312 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiadz29is/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiadz29is/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 5349582 5349839 - 5349325 3 chr1 5349582 5349839 - 5349581 0 chr1 5971841 5974958 - 5971584 1 chr1 5971841 5974958 - 5971840 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtkax5pv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtkax5pv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 5349582 5349839 - 5349325 3 chr1 5349582 5349839 - 5349581 0 chr1 5971841 5974958 - 5971584 1 chr1 5971841 5974958 - 5971840 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5349325 1 chr1 5349582 5349839 - 5349581 2 chr1 5971841 5974958 - 5971584 3 chr1 5971841 5974958 - 5971840 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9u0rbkuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9u0rbkuh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 5349582 5349839 - 5347363 3 chr1 5349582 5349839 - 5349325 0 chr1 5971841 5974958 - 5969622 1 chr1 5971841 5974958 - 5971584 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgk2bffno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgk2bffno/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5971841 | 5974958 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | | chr1 | 5349582 | 5349839 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 5349582 5349839 - 5347363 3 chr1 5349582 5349839 - 5349325 0 chr1 5971841 5974958 - 5969622 1 chr1 5971841 5974958 - 5971584 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349839 - 5347363 1 chr1 5349582 5349839 - 5349325 2 chr1 5971841 5974958 - 5969622 3 chr1 5971841 5974958 - 5971584 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphos278jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphos278jk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5349582 | 5349583 | a | 0 | ... | | chr1 | 5971841 | 5971842 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 df2 Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 Actual Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 Expected Chromosome Start End Strand Distance 0 chr1 5349582 5349583 + 5349325 1 chr1 5971841 5971842 - 5971584 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ri2x81k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ri2x81k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6393486 + 2240332 11 chr1 6384213 6393486 + 2476749 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6904736 | 6905014 | a | 0 | ... | | chr1 | 6904736 | 6905014 | a | 0 | ... | | chr1 | 1875948 | 1880403 | a | 0 | ... | | chr1 | 1875948 | 1880403 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1857885 | 1864713 | a | 0 | ... | | chr1 | 1857885 | 1864713 | a | 0 | ... | | chr1 | 7477081 | 7480654 | a | 0 | ... | | chr1 | 7477081 | 7480654 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr1 1857885 1864713 - 2269306 15 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 12 chr1 2585164 2593524 - 1540495 13 chr1 2585164 2593524 - 6276711 10 chr1 3120336 3130271 + 1003748 11 chr1 3120336 3130271 + 5739964 6 chr1 3977291 3986661 + 147358 7 chr1 3977291 3986661 + 4883574 8 chr1 6384213 6393486 + 2240332 9 chr1 6384213 6393486 + 2476749 0 chr1 6904736 6905014 + 1965221 1 chr1 6904736 6905014 + 2760855 16 chr1 7477081 7480654 - 1389581 17 chr1 7477081 7480654 - 3333200 4 chr1 8282853 8289660 + 580575 5 chr1 8282853 8289660 + 4138972 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6393486 + 2240332 11 chr1 6384213 6393486 + 2476749 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6393486 + 2240332 11 chr1 6384213 6393486 + 2476749 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6393486 + 2240332 11 chr1 6384213 6393486 + 2476749 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmcsuguxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcsuguxx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6384214 + 2240332 11 chr1 6384213 6384214 + 2486021 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6904736 | 6905014 | a | 0 | ... | | chr1 | 6904736 | 6905014 | a | 0 | ... | | chr1 | 1875948 | 1880403 | a | 0 | ... | | chr1 | 1875948 | 1880403 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1857885 | 1864713 | a | 0 | ... | | chr1 | 1857885 | 1864713 | a | 0 | ... | | chr1 | 7477081 | 7480654 | a | 0 | ... | | chr1 | 7477081 | 7480654 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr1 1857885 1864713 - 2269306 15 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 12 chr1 2585164 2593524 - 1540495 13 chr1 2585164 2593524 - 6276711 10 chr1 3120336 3130271 + 1003748 11 chr1 3120336 3130271 + 5739964 6 chr1 3977291 3986661 + 147358 7 chr1 3977291 3986661 + 4883574 8 chr1 6384213 6384214 + 2240332 9 chr1 6384213 6384214 + 2486021 0 chr1 6904736 6905014 + 1965221 1 chr1 6904736 6905014 + 2760855 16 chr1 7477081 7480654 - 1389581 17 chr1 7477081 7480654 - 3333200 4 chr1 8282853 8289660 + 580575 5 chr1 8282853 8289660 + 4138972 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6384214 + 2240332 11 chr1 6384213 6384214 + 2486021 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6384214 + 2240332 11 chr1 6384213 6384214 + 2486021 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1864713 - 2269306 1 chr1 1857885 1864713 - 7005522 2 chr1 1875948 1880403 + 2253616 3 chr1 1875948 1880403 + 6989832 4 chr1 2585164 2593524 - 1540495 5 chr1 2585164 2593524 - 6276711 6 chr1 3120336 3130271 + 1003748 7 chr1 3120336 3130271 + 5739964 8 chr1 3977291 3986661 + 147358 9 chr1 3977291 3986661 + 4883574 10 chr1 6384213 6384214 + 2240332 11 chr1 6384213 6384214 + 2486021 12 chr1 6904736 6905014 + 1965221 13 chr1 6904736 6905014 + 2760855 14 chr1 7477081 7480654 - 1389581 15 chr1 7477081 7480654 - 3333200 16 chr1 8282853 8289660 + 580575 17 chr1 8282853 8289660 + 4138972 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6xjwicu5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xjwicu5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1792312 1 chr1 1875948 1876205 - 1810375 2 chr1 2585164 2585165 - 2519591 3 chr1 3120336 3120344 - 3054763 4 chr1 3977291 3977298 - 3911718 5 chr1 6384213 6384470 - 6318640 6 chr1 6904736 6904744 - 6839163 7 chr1 7477081 7477089 - 7411508 8 chr1 8282853 8283110 - 8217280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2585164 | 2585165 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 6904736 | 6904744 | a | 0 | ... | | chr1 | 1875948 | 1876205 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3977291 | 3977298 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | | chr1 | 3120336 | 3120344 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1857885 1857886 - 1792312 3 chr1 1875948 1876205 - 1810375 0 chr1 2585164 2585165 - 2519591 8 chr1 3120336 3120344 - 3054763 5 chr1 3977291 3977298 - 3911718 7 chr1 6384213 6384470 - 6318640 2 chr1 6904736 6904744 - 6839163 6 chr1 7477081 7477089 - 7411508 4 chr1 8282853 8283110 - 8217280 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1792312 1 chr1 1875948 1876205 - 1810375 2 chr1 2585164 2585165 - 2519591 3 chr1 3120336 3120344 - 3054763 4 chr1 3977291 3977298 - 3911718 5 chr1 6384213 6384470 - 6318640 6 chr1 6904736 6904744 - 6839163 7 chr1 7477081 7477089 - 7411508 8 chr1 8282853 8283110 - 8217280 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1792312 1 chr1 1875948 1876205 - 1810375 2 chr1 2585164 2585165 - 2519591 3 chr1 3120336 3120344 - 3054763 4 chr1 3977291 3977298 - 3911718 5 chr1 6384213 6384470 - 6318640 6 chr1 6904736 6904744 - 6839163 7 chr1 7477081 7477089 - 7411508 8 chr1 8282853 8283110 - 8217280 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1792312 1 chr1 1875948 1876205 - 1810375 2 chr1 2585164 2585165 - 2519591 3 chr1 3120336 3120344 - 3054763 4 chr1 3977291 3977298 - 3911718 5 chr1 6384213 6384470 - 6318640 6 chr1 6904736 6904744 - 6839163 7 chr1 7477081 7477089 - 7411508 8 chr1 8282853 8283110 - 8217280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptzrv4g70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzrv4g70/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 2585164 2585165 - 2585163 3 chr1 3120336 3120344 - 3120335 4 chr1 3977291 3977298 - 3977290 5 chr1 6384213 6384470 - 6384212 6 chr1 6904736 6904744 - 6904735 7 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282852 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2585164 | 2585165 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 6904736 | 6904744 | a | 0 | ... | | chr1 | 1875948 | 1876205 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3977291 | 3977298 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | | chr1 | 3120336 | 3120344 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1857885 1857886 - 1857884 3 chr1 1875948 1876205 - 1875947 0 chr1 2585164 2585165 - 2585163 8 chr1 3120336 3120344 - 3120335 5 chr1 3977291 3977298 - 3977290 7 chr1 6384213 6384470 - 6384212 2 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 4 chr1 8282853 8283110 - 8282852 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 2585164 2585165 - 2585163 3 chr1 3120336 3120344 - 3120335 4 chr1 3977291 3977298 - 3977290 5 chr1 6384213 6384470 - 6384212 6 chr1 6904736 6904744 - 6904735 7 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282852 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 2585164 2585165 - 2585163 3 chr1 3120336 3120344 - 3120335 4 chr1 3977291 3977298 - 3977290 5 chr1 6384213 6384470 - 6384212 6 chr1 6904736 6904744 - 6904735 7 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282852 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 2585164 2585165 - 2585163 3 chr1 3120336 3120344 - 3120335 4 chr1 3977291 3977298 - 3977290 5 chr1 6384213 6384470 - 6384212 6 chr1 6904736 6904744 - 6904735 7 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282852 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsf01u1bh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsf01u1bh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 3120336 3120337 - 3120335 3 chr1 3977291 3977298 - 3977290 4 chr1 6384213 6384470 - 6384212 5 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 7 chr1 8282853 8283110 - 8282852 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3120336 | 3120337 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 6904736 | 6904744 | a | 0 | ... | | chr1 | 1875948 | 1876205 | a | 0 | ... | | chr1 | 8282853 | 8283110 | a | 0 | ... | | chr1 | 3977291 | 3977298 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1857885 1857886 - 1857884 3 chr1 1875948 1876205 - 1875947 0 chr1 3120336 3120337 - 3120335 5 chr1 3977291 3977298 - 3977290 7 chr1 6384213 6384470 - 6384212 2 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 4 chr1 8282853 8283110 - 8282852 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 3120336 3120337 - 3120335 3 chr1 3977291 3977298 - 3977290 4 chr1 6384213 6384470 - 6384212 5 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 7 chr1 8282853 8283110 - 8282852 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 3120336 3120337 - 3120335 3 chr1 3977291 3977298 - 3977290 4 chr1 6384213 6384470 - 6384212 5 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 7 chr1 8282853 8283110 - 8282852 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857884 1 chr1 1875948 1876205 - 1875947 2 chr1 3120336 3120337 - 3120335 3 chr1 3977291 3977298 - 3977290 4 chr1 6384213 6384470 - 6384212 5 chr1 6904736 6904744 - 6904735 6 chr1 7477081 7477089 - 7477080 7 chr1 8282853 8283110 - 8282852 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp84bzapq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp84bzapq4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857628 1 chr1 1857885 1857886 - 1857884 2 chr1 1875948 1876205 - 1875691 3 chr1 1875948 1876205 - 1875947 4 chr1 3120336 3120337 - 3120079 5 chr1 3120336 3120337 - 3120335 6 chr1 3977291 3977298 - 3977034 7 chr1 3977291 3977298 - 3977290 8 chr1 6384213 6384470 - 6383956 9 chr1 6384213 6384470 - 6384212 10 chr1 6904736 6904744 - 6904479 11 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 14 chr1 8282853 8283110 - 8282596 15 chr1 8282853 8283110 - 8282852 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3120336 | 3120337 | a | 0 | ... | | chr1 | 3120336 | 3120337 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1857885 1857886 - 1857628 3 chr1 1857885 1857886 - 1857884 6 chr1 1875948 1876205 - 1875691 7 chr1 1875948 1876205 - 1875947 0 chr1 3120336 3120337 - 3120079 1 chr1 3120336 3120337 - 3120335 10 chr1 3977291 3977298 - 3977034 11 chr1 3977291 3977298 - 3977290 14 chr1 6384213 6384470 - 6383956 15 chr1 6384213 6384470 - 6384212 4 chr1 6904736 6904744 - 6904479 5 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 8 chr1 8282853 8283110 - 8282596 9 chr1 8282853 8283110 - 8282852 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857628 1 chr1 1857885 1857886 - 1857884 2 chr1 1875948 1876205 - 1875691 3 chr1 1875948 1876205 - 1875947 4 chr1 3120336 3120337 - 3120079 5 chr1 3120336 3120337 - 3120335 6 chr1 3977291 3977298 - 3977034 7 chr1 3977291 3977298 - 3977290 8 chr1 6384213 6384470 - 6383956 9 chr1 6384213 6384470 - 6384212 10 chr1 6904736 6904744 - 6904479 11 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 14 chr1 8282853 8283110 - 8282596 15 chr1 8282853 8283110 - 8282852 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857628 1 chr1 1857885 1857886 - 1857884 2 chr1 1875948 1876205 - 1875691 3 chr1 1875948 1876205 - 1875947 4 chr1 3120336 3120337 - 3120079 5 chr1 3120336 3120337 - 3120335 6 chr1 3977291 3977298 - 3977034 7 chr1 3977291 3977298 - 3977290 8 chr1 6384213 6384470 - 6383956 9 chr1 6384213 6384470 - 6384212 10 chr1 6904736 6904744 - 6904479 11 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 14 chr1 8282853 8283110 - 8282596 15 chr1 8282853 8283110 - 8282852 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857628 1 chr1 1857885 1857886 - 1857884 2 chr1 1875948 1876205 - 1875691 3 chr1 1875948 1876205 - 1875947 4 chr1 3120336 3120337 - 3120079 5 chr1 3120336 3120337 - 3120335 6 chr1 3977291 3977298 - 3977034 7 chr1 3977291 3977298 - 3977290 8 chr1 6384213 6384470 - 6383956 9 chr1 6384213 6384470 - 6384212 10 chr1 6904736 6904744 - 6904479 11 chr1 6904736 6904744 - 6904735 12 chr1 7477081 7477089 - 7476824 13 chr1 7477081 7477089 - 7477080 14 chr1 8282853 8283110 - 8282596 15 chr1 8282853 8283110 - 8282852 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp23pgj_h8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23pgj_h8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857880 1 chr1 1875948 1876205 - 1875943 2 chr1 3120336 3120337 - 3120331 3 chr1 3977291 3977298 - 3977286 4 chr1 6384213 6384470 - 6384208 5 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 7 chr1 8282853 8283110 - 8282848 9 chr17 9999999 10000015 + 9999742 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3120336 | 3120337 | a | 0 | ... | | chr1 | 1857885 | 1857886 | a | 0 | ... | | chr1 | 6904736 | 6904744 | a | 0 | ... | | chr1 | 1875948 | 1876205 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8282853 | 8283110 | a | 0 | ... | | chr1 | 3977291 | 3977298 | a | 0 | ... | | chr1 | 7477081 | 7477089 | a | 0 | ... | | chr1 | 6384213 | 6384470 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1857885 1857886 - 1857880 3 chr1 1875948 1876205 - 1875943 0 chr1 3120336 3120337 - 3120331 5 chr1 3977291 3977298 - 3977286 7 chr1 6384213 6384470 - 6384208 2 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 4 chr1 8282853 8283110 - 8282848 8 chr17 9999999 10000015 + 9999742 df2 Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857880 1 chr1 1875948 1876205 - 1875943 2 chr1 3120336 3120337 - 3120331 3 chr1 3977291 3977298 - 3977286 4 chr1 6384213 6384470 - 6384208 5 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 7 chr1 8282853 8283110 - 8282848 9 chr17 9999999 10000015 + 9999742 Actual Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857880 1 chr1 1875948 1876205 - 1875943 2 chr1 3120336 3120337 - 3120331 3 chr1 3977291 3977298 - 3977286 4 chr1 6384213 6384470 - 6384208 5 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 7 chr1 8282853 8283110 - 8282848 8 chr17 9999999 10000015 + 9999742 Expected Chromosome Start End Strand Distance 0 chr1 1857885 1857886 - 1857880 1 chr1 1875948 1876205 - 1875943 2 chr1 3120336 3120337 - 3120331 3 chr1 3977291 3977298 - 3977286 4 chr1 6384213 6384470 - 6384208 5 chr1 6904736 6904744 - 6904731 6 chr1 7477081 7477089 - 7477076 7 chr1 8282853 8283110 - 8282848 8 chr17 9999999 10000015 + 9999742 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3nzs8dz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3nzs8dz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyehosf1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyehosf1f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwy342k63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwy342k63/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpry8w5jfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpry8w5jfc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 613905 1 chr1 5732391 5735056 - 1311126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9rtzccql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9rtzccql/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 1311126 1 chr1 5732391 5735056 - 1406376 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkkg_f163/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkg_f163/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5732391 | 5735056 | a | 0 | ... | | chr1 | 5732391 | 5735056 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 df2 Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 Actual Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 Expected Chromosome Start End Strand Distance 0 chr1 5732391 5735056 - 5732382 1 chr1 5732391 5735056 - 5732385 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppsiup88n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppsiup88n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr2 5 10 - 65528 4 chr2 65537 65545 + 65528 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 65537 | 65545 | a | 0 | ... | | chr2 | 5 | 10 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr2 5 10 - 65528 0 chr2 65537 65545 + 65528 df2 Chromosome Start End Strand Distance 3 chr2 5 10 - 65528 4 chr2 65537 65545 + 65528 Actual Chromosome Start End Strand Distance 0 chr2 5 10 - 65528 1 chr2 65537 65545 + 65528 Expected Chromosome Start End Strand Distance 0 chr2 5 10 - 65528 1 chr2 65537 65545 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyd3kyfc_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyd3kyfc_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 777296 | 778138 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 df2 Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 Actual Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 Expected Chromosome Start End Strand Distance 0 chr1 777296 778138 + 4428054 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3tug85_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3tug85_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj5p10xmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5p10xmb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2gz49d5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gz49d5n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ynbbluu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ynbbluu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmcmjevts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcmjevts/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvq0mquh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvq0mquh3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 df2 Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 Actual Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 Expected Chromosome Start End Strand Distance 0 chr1 1 7 + 251 1 chr1 6 7 - 251 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfql8qyi5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfql8qyi5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 1 chr1 2104303 2108644 - 2863760 2 chr1 2846879 2848496 - 2123908 3 chr1 4381746 4386060 - 586344 4 chr1 4492514 4499564 + 472840 5 chr1 8228265 8236308 - 3255861 6 chr1 9502681 9506995 + 4530277 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 7598 | a | 0 | ... | | chr1 | 4492514 | 4499564 | a | 0 | ... | | chr1 | 9502681 | 9506995 | a | 0 | ... | | chr1 | 8228265 | 8236308 | a | 0 | ... | | chr1 | 2846879 | 2848496 | a | 0 | ... | | chr1 | 4381746 | 4386060 | a | 0 | ... | | chr1 | 2104303 | 2108644 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 6 chr1 2104303 2108644 - 2863760 4 chr1 2846879 2848496 - 2123908 5 chr1 4381746 4386060 - 586344 1 chr1 4492514 4499564 + 472840 3 chr1 8228265 8236308 - 3255861 2 chr1 9502681 9506995 + 4530277 df2 Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 1 chr1 2104303 2108644 - 2863760 2 chr1 2846879 2848496 - 2123908 3 chr1 4381746 4386060 - 586344 4 chr1 4492514 4499564 + 472840 5 chr1 8228265 8236308 - 3255861 6 chr1 9502681 9506995 + 4530277 Actual Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 1 chr1 2104303 2108644 - 2863760 2 chr1 2846879 2848496 - 2123908 3 chr1 4381746 4386060 - 586344 4 chr1 4492514 4499564 + 472840 5 chr1 8228265 8236308 - 3255861 6 chr1 9502681 9506995 + 4530277 Expected Chromosome Start End Strand Distance 0 chr1 1 7598 + 4964806 1 chr1 2104303 2108644 - 2863760 2 chr1 2846879 2848496 - 2123908 3 chr1 4381746 4386060 - 586344 4 chr1 4492514 4499564 + 472840 5 chr1 8228265 8236308 - 3255861 6 chr1 9502681 9506995 + 4530277 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyh56lv8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyh56lv8h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 2 chr1 1 3 - 1 3 chr1 1 3 - 938 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 57492 9 chr1 65537 65539 + 64595 10 chr1 65537 65539 + 57492 11 chr1 65537 65539 + 64595 12 chr1 65537 65539 - 57492 13 chr1 65537 65539 - 64595 14 chr1 65537 65539 - 57492 15 chr1 65537 65539 - 64595 16 chr1 65537 65539 - 57492 17 chr1 65537 65539 - 64595 18 chr1 65537 65539 - 57492 19 chr1 65537 65539 - 64595 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 3 - 1 7 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 10 chr1 2 4 - 937 11 chr1 2 4 - 8040 16 chr1 4 6 - 935 17 chr1 4 6 - 8038 0 chr1 65537 65539 + 57492 4 chr1 65537 65539 + 57492 8 chr1 65537 65539 - 57492 12 chr1 65537 65539 - 57492 14 chr1 65537 65539 - 57492 18 chr1 65537 65539 - 57492 1 chr1 65537 65539 + 64595 5 chr1 65537 65539 + 64595 9 chr1 65537 65539 - 64595 13 chr1 65537 65539 - 64595 15 chr1 65537 65539 - 64595 19 chr1 65537 65539 - 64595 df2 Chromosome Start End Strand Distance 2 chr1 1 3 - 1 3 chr1 1 3 - 938 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 57492 10 chr1 65537 65539 + 57492 12 chr1 65537 65539 - 57492 14 chr1 65537 65539 - 57492 16 chr1 65537 65539 - 57492 18 chr1 65537 65539 - 57492 9 chr1 65537 65539 + 64595 11 chr1 65537 65539 + 64595 13 chr1 65537 65539 - 64595 15 chr1 65537 65539 - 64595 17 chr1 65537 65539 - 64595 19 chr1 65537 65539 - 64595 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 57492 9 chr1 65537 65539 + 57492 10 chr1 65537 65539 + 64595 11 chr1 65537 65539 + 64595 12 chr1 65537 65539 - 57492 13 chr1 65537 65539 - 57492 14 chr1 65537 65539 - 57492 15 chr1 65537 65539 - 57492 16 chr1 65537 65539 - 64595 17 chr1 65537 65539 - 64595 18 chr1 65537 65539 - 64595 19 chr1 65537 65539 - 64595 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 57492 9 chr1 65537 65539 + 57492 10 chr1 65537 65539 + 64595 11 chr1 65537 65539 + 64595 12 chr1 65537 65539 - 57492 13 chr1 65537 65539 - 57492 14 chr1 65537 65539 - 57492 15 chr1 65537 65539 - 57492 16 chr1 65537 65539 - 64595 17 chr1 65537 65539 - 64595 18 chr1 65537 65539 - 64595 19 chr1 65537 65539 - 64595 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4l4hs22d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4l4hs22d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 2 chr1 1 3 - 1 3 chr1 1 3 - 938 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 49452 9 chr1 65537 65539 + 63658 10 chr1 65537 65539 + 49452 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 49452 13 chr1 65537 65539 - 63658 14 chr1 65537 65539 - 49452 15 chr1 65537 65539 - 63658 16 chr1 65537 65539 - 49452 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 49452 19 chr1 65537 65539 - 63658 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 3 - 1 7 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 10 chr1 2 4 - 937 11 chr1 2 4 - 8040 16 chr1 4 6 - 935 17 chr1 4 6 - 8038 0 chr1 65537 65539 + 49452 4 chr1 65537 65539 + 49452 8 chr1 65537 65539 - 49452 12 chr1 65537 65539 - 49452 14 chr1 65537 65539 - 49452 18 chr1 65537 65539 - 49452 1 chr1 65537 65539 + 63658 5 chr1 65537 65539 + 63658 9 chr1 65537 65539 - 63658 13 chr1 65537 65539 - 63658 15 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 df2 Chromosome Start End Strand Distance 2 chr1 1 3 - 1 3 chr1 1 3 - 938 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 49452 10 chr1 65537 65539 + 49452 12 chr1 65537 65539 - 49452 14 chr1 65537 65539 - 49452 16 chr1 65537 65539 - 49452 18 chr1 65537 65539 - 49452 9 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 13 chr1 65537 65539 - 63658 15 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 49452 9 chr1 65537 65539 + 49452 10 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 49452 13 chr1 65537 65539 - 49452 14 chr1 65537 65539 - 49452 15 chr1 65537 65539 - 49452 16 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 937 5 chr1 2 4 - 8040 6 chr1 4 6 - 935 7 chr1 4 6 - 8038 8 chr1 65537 65539 + 49452 9 chr1 65537 65539 + 49452 10 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 49452 13 chr1 65537 65539 - 49452 14 chr1 65537 65539 - 49452 15 chr1 65537 65539 - 49452 16 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy3vp07lp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3vp07lp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 2 chr1 1 3 - 1 3 chr1 1 3 - 938 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 57494 9 chr1 65537 65539 + 63658 10 chr1 65537 65539 + 57494 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 57494 13 chr1 65537 65539 - 63658 14 chr1 65537 65539 - 57494 15 chr1 65537 65539 - 63658 16 chr1 65537 65539 - 57494 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 57494 19 chr1 65537 65539 - 63658 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 3 - 1 7 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 10 chr1 2 4 - 1 11 chr1 2 4 - 937 16 chr1 4 6 - 3 17 chr1 4 6 - 935 0 chr1 65537 65539 + 57494 4 chr1 65537 65539 + 57494 8 chr1 65537 65539 - 57494 12 chr1 65537 65539 - 57494 14 chr1 65537 65539 - 57494 18 chr1 65537 65539 - 57494 1 chr1 65537 65539 + 63658 5 chr1 65537 65539 + 63658 9 chr1 65537 65539 - 63658 13 chr1 65537 65539 - 63658 15 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 df2 Chromosome Start End Strand Distance 2 chr1 1 3 - 1 3 chr1 1 3 - 938 0 chr1 1 258 + 683 1 chr1 1 258 + 7786 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 57494 10 chr1 65537 65539 + 57494 12 chr1 65537 65539 - 57494 14 chr1 65537 65539 - 57494 16 chr1 65537 65539 - 57494 18 chr1 65537 65539 - 57494 9 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 13 chr1 65537 65539 - 63658 15 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 57494 9 chr1 65537 65539 + 57494 10 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 57494 13 chr1 65537 65539 - 57494 14 chr1 65537 65539 - 57494 15 chr1 65537 65539 - 57494 16 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 7786 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 57494 9 chr1 65537 65539 + 57494 10 chr1 65537 65539 + 63658 11 chr1 65537 65539 + 63658 12 chr1 65537 65539 - 57494 13 chr1 65537 65539 - 57494 14 chr1 65537 65539 - 57494 15 chr1 65537 65539 - 57494 16 chr1 65537 65539 - 63658 17 chr1 65537 65539 - 63658 18 chr1 65537 65539 - 63658 19 chr1 65537 65539 - 63658 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg4v67ls4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4v67ls4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 683 1 chr1 1 258 + 6793 2 chr1 1 3 - 1 3 chr1 1 3 - 938 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 48370 9 chr1 65537 65539 + 51438 10 chr1 65537 65539 + 48370 11 chr1 65537 65539 + 51438 12 chr1 65537 65539 - 48370 13 chr1 65537 65539 - 51438 14 chr1 65537 65539 - 48370 15 chr1 65537 65539 - 51438 16 chr1 65537 65539 - 48370 17 chr1 65537 65539 - 51438 18 chr1 65537 65539 - 48370 19 chr1 65537 65539 - 51438 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 4 | 6 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 3 - 1 7 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 6793 10 chr1 2 4 - 1 11 chr1 2 4 - 937 16 chr1 4 6 - 3 17 chr1 4 6 - 935 0 chr1 65537 65539 + 48370 4 chr1 65537 65539 + 48370 8 chr1 65537 65539 - 48370 12 chr1 65537 65539 - 48370 14 chr1 65537 65539 - 48370 18 chr1 65537 65539 - 48370 1 chr1 65537 65539 + 51438 5 chr1 65537 65539 + 51438 9 chr1 65537 65539 - 51438 13 chr1 65537 65539 - 51438 15 chr1 65537 65539 - 51438 19 chr1 65537 65539 - 51438 df2 Chromosome Start End Strand Distance 2 chr1 1 3 - 1 3 chr1 1 3 - 938 0 chr1 1 258 + 683 1 chr1 1 258 + 6793 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 48370 10 chr1 65537 65539 + 48370 12 chr1 65537 65539 - 48370 14 chr1 65537 65539 - 48370 16 chr1 65537 65539 - 48370 18 chr1 65537 65539 - 48370 9 chr1 65537 65539 + 51438 11 chr1 65537 65539 + 51438 13 chr1 65537 65539 - 51438 15 chr1 65537 65539 - 51438 17 chr1 65537 65539 - 51438 19 chr1 65537 65539 - 51438 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 6793 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 48370 9 chr1 65537 65539 + 48370 10 chr1 65537 65539 + 51438 11 chr1 65537 65539 + 51438 12 chr1 65537 65539 - 48370 13 chr1 65537 65539 - 48370 14 chr1 65537 65539 - 48370 15 chr1 65537 65539 - 48370 16 chr1 65537 65539 - 51438 17 chr1 65537 65539 - 51438 18 chr1 65537 65539 - 51438 19 chr1 65537 65539 - 51438 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 1 1 chr1 1 3 - 938 2 chr1 1 258 + 683 3 chr1 1 258 + 6793 4 chr1 2 4 - 1 5 chr1 2 4 - 937 6 chr1 4 6 - 3 7 chr1 4 6 - 935 8 chr1 65537 65539 + 48370 9 chr1 65537 65539 + 48370 10 chr1 65537 65539 + 51438 11 chr1 65537 65539 + 51438 12 chr1 65537 65539 - 48370 13 chr1 65537 65539 - 48370 14 chr1 65537 65539 - 48370 15 chr1 65537 65539 - 48370 16 chr1 65537 65539 - 51438 17 chr1 65537 65539 - 51438 18 chr1 65537 65539 - 51438 19 chr1 65537 65539 - 51438 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpecl1m2m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpecl1m2m4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 939 2 chr1 1 2 - 2 3 chr1 1 2 - 939 4 chr1 1 2 - 2 5 chr1 1 2 - 939 6 chr1 1 2 - 2 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9502681 | 9502684 | a | 0 | ... | | chr1 | 9502681 | 9502684 | a | 0 | ... | | chr1 | 8584 | 17168 | a | 0 | ... | | chr1 | 8584 | 17168 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 12 chr1 1 2 - 2 14 chr1 1 2 - 2 16 chr1 1 2 - 2 18 chr1 1 2 - 2 13 chr1 1 2 - 939 15 chr1 1 2 - 939 17 chr1 1 2 - 939 19 chr1 1 2 - 939 10 chr1 3 6 - 2 11 chr1 3 6 - 935 4 chr1 940 1880 - 935 5 chr1 940 1880 - 939 8 chr1 7050 14100 - 5171 9 chr1 7050 14100 - 7045 6 chr1 8043 8044 - 541 7 chr1 8043 8044 - 6164 2 chr1 8584 17168 - 541 3 chr1 8584 17168 - 6705 0 chr1 9502681 9502684 - 9485514 1 chr1 9502681 9502684 - 9488582 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 2 chr1 1 2 - 2 4 chr1 1 2 - 2 6 chr1 1 2 - 2 1 chr1 1 2 - 939 3 chr1 1 2 - 939 5 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 939 5 chr1 1 2 - 939 6 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 939 5 chr1 1 2 - 939 6 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgw6u7yog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgw6u7yog/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 939 2 chr1 1 2 - 2 3 chr1 1 2 - 939 4 chr1 1 2 - 2 5 chr1 1 2 - 939 6 chr1 1 2 - 2 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9502681 | 9502684 | a | 0 | ... | | chr1 | 9502681 | 9502684 | a | 0 | ... | | chr1 | 8584 | 17168 | a | 0 | ... | | chr1 | 8584 | 17168 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 20 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 12 chr1 1 2 - 2 14 chr1 1 2 - 2 16 chr1 1 2 - 2 18 chr1 1 2 - 2 13 chr1 1 2 - 939 15 chr1 1 2 - 939 17 chr1 1 2 - 939 19 chr1 1 2 - 939 10 chr1 3 6 - 2 11 chr1 3 6 - 935 4 chr1 940 1880 - 935 5 chr1 940 1880 - 939 8 chr1 7050 14100 - 5171 9 chr1 7050 14100 - 7045 6 chr1 8043 8044 - 541 7 chr1 8043 8044 - 6164 2 chr1 8584 17168 - 541 3 chr1 8584 17168 - 6705 0 chr1 9502681 9502684 - 9485514 1 chr1 9502681 9502684 - 9488582 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 2 chr1 1 2 - 2 4 chr1 1 2 - 2 6 chr1 1 2 - 2 1 chr1 1 2 - 939 3 chr1 1 2 - 939 5 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 939 5 chr1 1 2 - 939 6 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 939 5 chr1 1 2 - 939 6 chr1 1 2 - 939 7 chr1 1 2 - 939 8 chr1 3 6 - 2 9 chr1 3 6 - 935 10 chr1 940 1880 - 935 11 chr1 940 1880 - 939 12 chr1 7050 14100 - 5171 13 chr1 7050 14100 - 7045 14 chr1 8043 8044 - 541 15 chr1 8043 8044 - 6164 16 chr1 8584 17168 - 541 17 chr1 8584 17168 - 6705 18 chr1 9502681 9502684 - 9485514 19 chr1 9502681 9502684 - 9488582 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=20, step=1) Expected index RangeIndex(start=0, stop=20, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7rnfspqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7rnfspqa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpobiuvoab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobiuvoab/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa2rn94b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2rn94b3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_lgcsesu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_lgcsesu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt7glub96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7glub96/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_z4o0928/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_z4o0928/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2137398 - 1758191 1 chr1 2130767 2137398 - 3215459 2 chr1 5054106 5057810 + 295047 3 chr1 5054106 5057810 + 1150943 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5054106 | 5057810 | a | 0 | ... | | chr1 | 5054106 | 5057810 | a | 0 | ... | | chr1 | 2130767 | 2137398 | a | 0 | ... | | chr1 | 2130767 | 2137398 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2130767 2137398 - 1758191 3 chr1 2130767 2137398 - 3215459 0 chr1 5054106 5057810 + 295047 1 chr1 5054106 5057810 + 1150943 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2137398 - 1758191 1 chr1 2130767 2137398 - 3215459 2 chr1 5054106 5057810 + 295047 3 chr1 5054106 5057810 + 1150943 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2137398 - 1758191 1 chr1 2130767 2137398 - 3215459 2 chr1 5054106 5057810 + 295047 3 chr1 5054106 5057810 + 1150943 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2137398 - 1758191 1 chr1 2130767 2137398 - 3215459 2 chr1 5054106 5057810 + 295047 3 chr1 5054106 5057810 + 1150943 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9zisne_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zisne_d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpli72lv_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpli72lv_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph5t67q4c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5t67q4c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe6e4grrt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6e4grrt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 1236440 1 chr1 2130767 2130768 - 1236440 2 chr1 2130767 2130768 - 1236440 3 chr1 2130767 2130768 - 1236440 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9voarufd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9voarufd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 1 chr1 2130767 2130768 + 2130766 2 chr1 2130767 2130768 - 2130765 3 chr1 2130767 2130768 - 2130766 4 chr1 2130767 2130768 - 2130765 5 chr1 2130767 2130768 - 2130766 6 chr1 2130767 2130768 - 2130765 7 chr1 2130767 2130768 - 2130766 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | | chr1 | 2130767 | 2130768 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 2 chr1 2130767 2130768 - 2130765 4 chr1 2130767 2130768 - 2130765 6 chr1 2130767 2130768 - 2130765 1 chr1 2130767 2130768 + 2130766 3 chr1 2130767 2130768 - 2130766 5 chr1 2130767 2130768 - 2130766 7 chr1 2130767 2130768 - 2130766 df2 Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 2 chr1 2130767 2130768 - 2130765 4 chr1 2130767 2130768 - 2130765 6 chr1 2130767 2130768 - 2130765 1 chr1 2130767 2130768 + 2130766 3 chr1 2130767 2130768 - 2130766 5 chr1 2130767 2130768 - 2130766 7 chr1 2130767 2130768 - 2130766 Actual Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 1 chr1 2130767 2130768 + 2130766 2 chr1 2130767 2130768 - 2130765 3 chr1 2130767 2130768 - 2130765 4 chr1 2130767 2130768 - 2130765 5 chr1 2130767 2130768 - 2130766 6 chr1 2130767 2130768 - 2130766 7 chr1 2130767 2130768 - 2130766 Expected Chromosome Start End Strand Distance 0 chr1 2130767 2130768 + 2130765 1 chr1 2130767 2130768 + 2130766 2 chr1 2130767 2130768 - 2130765 3 chr1 2130767 2130768 - 2130765 4 chr1 2130767 2130768 - 2130765 5 chr1 2130767 2130768 - 2130766 6 chr1 2130767 2130768 - 2130766 7 chr1 2130767 2130768 - 2130766 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpay0xt8gp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpay0xt8gp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 14 chrX 5845437 5845723 - 449422 15 chrX 7883280 7888139 - 2487265 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 9587 + 660069 5 chr1 2 9587 + 1209178 6 chr1 5416362 5422259 - 1826971 7 chr1 5416362 5422259 - 3815027 10 chrX 5845437 5845723 - 449422 2 chr1 7107361 7116114 + 133116 3 chr1 7107361 7116114 + 2121172 11 chrX 7883280 7888139 - 2487265 0 chr1 8425326 8429580 + 807706 1 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 df2 Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 14 chrX 5845437 5845723 - 449422 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 15 chrX 7883280 7888139 - 2487265 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 Actual Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 10 chrX 5845437 5845723 - 449422 11 chrX 7883280 7888139 - 2487265 Expected Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 10 chrX 5845437 5845723 - 449422 11 chrX 7883280 7888139 - 2487265 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzdpuopha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzdpuopha/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 14 chrX 5845437 5845723 - 449422 15 chrX 7883280 7888139 - 2487265 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 9587 + 660069 5 chr1 2 9587 + 1209178 6 chr1 5416362 5422259 - 1826971 7 chr1 5416362 5422259 - 3815027 10 chrX 5845437 5845723 - 449422 2 chr1 7107361 7116114 + 133116 3 chr1 7107361 7116114 + 2121172 11 chrX 7883280 7888139 - 2487265 0 chr1 8425326 8429580 + 807706 1 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 df2 Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 14 chrX 5845437 5845723 - 449422 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 15 chrX 7883280 7888139 - 2487265 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 Actual Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 10 chrX 5845437 5845723 - 449422 11 chrX 7883280 7888139 - 2487265 Expected Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 1826971 3 chr1 5416362 5422259 - 3815027 4 chr1 7107361 7116114 + 133116 5 chr1 7107361 7116114 + 2121172 6 chr1 8425326 8429580 + 807706 7 chr1 8425326 8429580 + 1171600 8 chr1 8594015 8598239 - 639047 9 chr1 8594015 8598239 - 1340289 10 chrX 5845437 5845723 - 449422 11 chrX 7883280 7888139 - 2487265 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3hk7tvit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3hk7tvit/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 4197598 3 chr1 5416362 5422259 - 4577742 4 chr1 7107361 7116114 + 2883887 5 chr1 7107361 7116114 + 5888597 6 chr1 8425326 8429580 + 1570421 7 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 14 chrX 5845437 5845723 - 448148 15 chrX 7883280 7888139 - 2485991 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 8425326 | 8429580 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | chr1 | 7107361 | 7116114 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 5416362 | 5422259 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | | chr1 | 8594015 | 8598239 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 9587 + 660069 5 chr1 2 9587 + 1209178 6 chr1 5416362 5422259 - 4197598 7 chr1 5416362 5422259 - 4577742 10 chrX 5845437 5845723 - 448148 2 chr1 7107361 7116114 + 2883887 3 chr1 7107361 7116114 + 5888597 11 chrX 7883280 7888139 - 2485991 0 chr1 8425326 8429580 + 1570421 1 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 df2 Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 4197598 3 chr1 5416362 5422259 - 4577742 14 chrX 5845437 5845723 - 448148 4 chr1 7107361 7116114 + 2883887 5 chr1 7107361 7116114 + 5888597 15 chrX 7883280 7888139 - 2485991 6 chr1 8425326 8429580 + 1570421 7 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 Actual Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 4197598 3 chr1 5416362 5422259 - 4577742 4 chr1 7107361 7116114 + 2883887 5 chr1 7107361 7116114 + 5888597 6 chr1 8425326 8429580 + 1570421 7 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 10 chrX 5845437 5845723 - 448148 11 chrX 7883280 7888139 - 2485991 Expected Chromosome Start End Strand Distance 0 chr1 2 9587 + 660069 1 chr1 2 9587 + 1209178 2 chr1 5416362 5422259 - 4197598 3 chr1 5416362 5422259 - 4577742 4 chr1 7107361 7116114 + 2883887 5 chr1 7107361 7116114 + 5888597 6 chr1 8425326 8429580 + 1570421 7 chr1 8425326 8429580 + 7206562 8 chr1 8594015 8598239 - 1401762 9 chr1 8594015 8598239 - 7375251 10 chrX 5845437 5845723 - 448148 11 chrX 7883280 7888139 - 2485991 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsn55dokh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsn55dokh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 7 1 chr1 6 7 - 4 2 chr1 6 7 - 4 3 chr1 6 7 - 4 4 chr1 6 7 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjpaujdij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpaujdij/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr2 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmk7yzyv8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk7yzyv8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr2 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyb1445s0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyb1445s0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr2 | 6 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 6 chr2 6 7 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 6 7 - 65531 2 chr1 6 7 - 65531 3 chr1 6 7 - 65531 4 chr1 6 7 - 65531 5 chr2 6 7 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzm2o22th/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzm2o22th/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplu45ue01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplu45ue01/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpypn6_nmu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpypn6_nmu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwykrezjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwykrezjf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr19 | 2455990 | 2458227 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 df2 Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 Actual Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 Expected Chromosome Start End Strand Distance 0 chr19 2455990 2458227 - 2390197 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxeqvv6to/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxeqvv6to/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7548952 | 7549025 | a | 0 | ... | | chr1 | 7548952 | 7549025 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 df2 Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Actual Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Expected Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpltnbh9u0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpltnbh9u0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7548952 | 7549025 | a | 0 | ... | | chr1 | 7548952 | 7549025 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 df2 Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Actual Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Expected Chromosome Start End Strand Distance 0 chr1 7548952 7549025 + 7548690 1 chr1 7548952 7549025 + 7548693 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpktx9x0iz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktx9x0iz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 7548952 | 7549025 | a | 0 | ... | | chr1 | 7548952 | 7549025 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 df2 Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 2 1 chr1 7548952 7549025 + 7548690 2 chr1 7548952 7549025 + 7548693 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00plyybe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00plyybe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmm4aumit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmm4aumit/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz5h5btoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5h5btoh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf48q4iru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf48q4iru/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 + 93 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 + 93 df2 Chromosome Start End Strand Distance 0 chr2 1 2 + 93 Actual Chromosome Start End Strand Distance 0 chr2 1 2 + 93 Expected Chromosome Start End Strand Distance 0 chr2 1 2 + 93 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp375pgjgq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp375pgjgq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxo23cb4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxo23cb4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsvorbd67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvorbd67/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 df2 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 Actual Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 Expected Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 590737 1 chr1 8418604 8423985 - 1889163 2 chr1 8875211 8875552 - 139170 3 chr1 8875211 8875552 - 2345770 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_lc4qcs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_lc4qcs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 df2 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 Actual Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 Expected Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8353067 1 chr1 8418604 8423985 - 8416156 2 chr1 8875211 8875552 - 8809674 3 chr1 8875211 8875552 - 8872763 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppobfqim6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppobfqim6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8418604 | 8423985 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | | chr1 | 8875211 | 8875552 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 df2 Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 Actual Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 Expected Chromosome Start End Strand Distance 0 chr1 8418604 8423985 - 8418346 1 chr1 8418604 8423985 - 8418580 2 chr1 8875211 8875552 - 8874953 3 chr1 8875211 8875552 - 8875187 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv778fq_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv778fq_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb324fvve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb324fvve/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 25 + 22 1 chr1 2 25 + 65513 2 chr1 2 259 - 65279 3 chr1 2 3 - 21 4 chr1 2 3 - 44 5 chr1 2 5 - 19 6 chr1 2 5 - 42 7 chr1 2 5 - 19 8 chr1 2 5 - 42 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 25 | a | 0 | ... | | chr1 | 2 | 25 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 5 | a | 0 | ... | | chr1 | 2 | 5 | a | 0 | ... | | chr1 | 2 | 5 | a | 0 | ... | | chr1 | 2 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2 3 - 21 3 chr1 2 3 - 44 5 chr1 2 5 - 19 7 chr1 2 5 - 19 6 chr1 2 5 - 42 8 chr1 2 5 - 42 0 chr1 2 25 + 22 1 chr1 2 25 + 65513 4 chr1 2 259 - 65279 df2 Chromosome Start End Strand Distance 3 chr1 2 3 - 21 4 chr1 2 3 - 44 5 chr1 2 5 - 19 7 chr1 2 5 - 19 6 chr1 2 5 - 42 8 chr1 2 5 - 42 0 chr1 2 25 + 22 1 chr1 2 25 + 65513 2 chr1 2 259 - 65279 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 21 1 chr1 2 3 - 44 2 chr1 2 5 - 19 3 chr1 2 5 - 19 4 chr1 2 5 - 42 5 chr1 2 5 - 42 6 chr1 2 25 + 22 7 chr1 2 25 + 65513 8 chr1 2 259 - 65279 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 21 1 chr1 2 3 - 44 2 chr1 2 5 - 19 3 chr1 2 5 - 19 4 chr1 2 5 - 42 5 chr1 2 5 - 42 6 chr1 2 25 + 22 7 chr1 2 25 + 65513 8 chr1 2 259 - 65279 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp12_tjy1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12_tjy1j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 43 4 chr1 1 4 - 20 5 chr1 1 4 - 43 6 chr1 1 4 - 20 7 chr1 1 4 - 43 8 chr1 65537 65540 - 65235 9 chr1 65537 65540 - 65258 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 + 20 4 chr1 1 4 - 20 6 chr1 1 4 - 20 8 chr1 1 4 - 20 1 chr1 1 4 + 43 5 chr1 1 4 - 43 7 chr1 1 4 - 43 9 chr1 1 4 - 43 2 chr1 65537 65540 - 65235 3 chr1 65537 65540 - 65258 df2 Chromosome Start End Strand Distance 0 chr1 1 4 + 20 2 chr1 1 4 - 20 4 chr1 1 4 - 20 6 chr1 1 4 - 20 1 chr1 1 4 + 43 3 chr1 1 4 - 43 5 chr1 1 4 - 43 7 chr1 1 4 - 43 8 chr1 65537 65540 - 65235 9 chr1 65537 65540 - 65258 Actual Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 20 4 chr1 1 4 - 20 5 chr1 1 4 - 43 6 chr1 1 4 - 43 7 chr1 1 4 - 43 8 chr1 65537 65540 - 65235 9 chr1 65537 65540 - 65258 Expected Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 20 4 chr1 1 4 - 20 5 chr1 1 4 - 43 6 chr1 1 4 - 43 7 chr1 1 4 - 43 8 chr1 65537 65540 - 65235 9 chr1 65537 65540 - 65258 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpce6q6kr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpce6q6kr5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 43 4 chr1 1 4 - 20 5 chr1 1 4 - 43 6 chr1 65537 65540 - 65235 7 chr1 65537 65540 - 65258 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 + 20 4 chr1 1 4 - 20 6 chr1 1 4 - 20 1 chr1 1 4 + 43 5 chr1 1 4 - 43 7 chr1 1 4 - 43 2 chr1 65537 65540 - 65235 3 chr1 65537 65540 - 65258 df2 Chromosome Start End Strand Distance 0 chr1 1 4 + 20 2 chr1 1 4 - 20 4 chr1 1 4 - 20 1 chr1 1 4 + 43 3 chr1 1 4 - 43 5 chr1 1 4 - 43 6 chr1 65537 65540 - 65235 7 chr1 65537 65540 - 65258 Actual Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 20 4 chr1 1 4 - 43 5 chr1 1 4 - 43 6 chr1 65537 65540 - 65235 7 chr1 65537 65540 - 65258 Expected Chromosome Start End Strand Distance 0 chr1 1 4 + 20 1 chr1 1 4 + 43 2 chr1 1 4 - 20 3 chr1 1 4 - 20 4 chr1 1 4 - 43 5 chr1 1 4 - 43 6 chr1 65537 65540 - 65235 7 chr1 65537 65540 - 65258 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9nm24h4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9nm24h4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6272248 6273856 + 1900002 1 chr1 6272248 6273856 + 5962055 2 chr1 8959181 8968729 + 4586935 3 chr1 8959181 8968729 + 8648988 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8959181 | 8968729 | a | 0 | ... | | chr1 | 8959181 | 8968729 | a | 0 | ... | | chr1 | 6272248 | 6273856 | a | 0 | ... | | chr1 | 6272248 | 6273856 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 6272248 6273856 + 1900002 3 chr1 6272248 6273856 + 5962055 0 chr1 8959181 8968729 + 4586935 1 chr1 8959181 8968729 + 8648988 df2 Chromosome Start End Strand Distance 0 chr1 6272248 6273856 + 1900002 1 chr1 6272248 6273856 + 5962055 2 chr1 8959181 8968729 + 4586935 3 chr1 8959181 8968729 + 8648988 Actual Chromosome Start End Strand Distance 0 chr1 6272248 6273856 + 1900002 1 chr1 6272248 6273856 + 5962055 2 chr1 8959181 8968729 + 4586935 3 chr1 8959181 8968729 + 8648988 Expected Chromosome Start End Strand Distance 0 chr1 6272248 6273856 + 1900002 1 chr1 6272248 6273856 + 5962055 2 chr1 8959181 8968729 + 4586935 3 chr1 8959181 8968729 + 8648988 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfhqgbt7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfhqgbt7o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8i_qlnt7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8i_qlnt7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp26a9vhm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp26a9vhm5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 + 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9v15oe9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9v15oe9w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0p8y9gqw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0p8y9gqw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 8959181 | 8959182 | a | 0 | ... | | chr2 | 8959181 | 8967298 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 df2 Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Actual Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Expected Chromosome Start End Strand Distance 0 chr2 8959181 8959182 - 8958888 1 chr2 8959181 8967298 - 8958888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjkd640u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjkd640u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp03am2lqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03am2lqm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4642731 | 4648603 | a | 0 | ... | | chr1 | 4642731 | 4648603 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 df2 Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 Actual Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 Expected Chromosome Start End Strand Distance 0 chr1 4642731 4648603 + 4488875 1 chr1 4642731 4648603 + 4750197 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnliyq8o8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnliyq8o8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw2bn1gw3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw2bn1gw3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqvl1z0i5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvl1z0i5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1zgwlx31/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zgwlx31/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 df2 Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 Actual Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 Expected Chromosome Start End Strand Distance 0 chr2 2 3 - 65535 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7322hhha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7322hhha/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv0st42zh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv0st42zh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5362ci3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5362ci3q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5jwkvyxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jwkvyxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 1352073 1 chr1 4459968 4460256 + 1721226 2 chr1 4614322 4621281 + 1506427 3 chr1 4614322 4621281 + 1875580 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqx9gks2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqx9gks2q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4614322 4621281 + 154067 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp54f1ks3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54f1ks3l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4459968 | 4460256 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4460256 + 154067 1 chr1 4459968 4460256 + 3895398 2 chr1 4614322 4621281 + 154067 3 chr1 4614322 4621281 + 3734373 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp03hxiw0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp03hxiw0j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4459970 | a | 0 | ... | | chr1 | 4459968 | 4459970 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 4394431 1 chr1 4459968 4459970 + 5540030 2 chr1 4614322 4621281 + 154354 3 chr1 4614322 4621281 + 4548785 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpji1he918/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpji1he918/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4459968 | 4459970 | a | 0 | ... | | chr1 | 4614322 | 4621281 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 df2 Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 Actual Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 Expected Chromosome Start End Strand Distance 0 chr1 4459968 4459970 + 154353 1 chr1 4614322 4621281 + 154353 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbck7zsql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbck7zsql/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 4614322 4621281 + 154353 2 chr8 8355653 8355655 + 3734373 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4614322 | 4621281 | a | 0 | ... | | chr8 | 8355653 | 8355655 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4614322 4621281 + 154353 1 chr8 8355653 8355655 + 3734373 df2 Chromosome Start End Strand Distance 1 chr1 4614322 4621281 + 154353 2 chr8 8355653 8355655 + 3734373 Actual Chromosome Start End Strand Distance 0 chr1 4614322 4621281 + 154353 1 chr8 8355653 8355655 + 3734373 Expected Chromosome Start End Strand Distance 0 chr1 4614322 4621281 + 154353 1 chr8 8355653 8355655 + 3734373 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjvqmhrvt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvqmhrvt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4238 | a | 0 | ... | | chr1 | 519643 | 529390 | a | 0 | ... | | chr1 | 9778855 | 9788814 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 df2 Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 Actual Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 Expected Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 519643 529390 - 339376 2 chr1 9778855 9788814 - 9598588 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuovzavji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuovzavji/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4238 | a | 0 | ... | | chr1 | 1 | 4238 | a | 0 | ... | | chr1 | 519643 | 529390 | a | 0 | ... | | chr1 | 519643 | 529390 | a | 0 | ... | | chr1 | 9778855 | 9788814 | a | 0 | ... | | chr1 | 9778855 | 9788814 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 df2 Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 Actual Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 Expected Chromosome Start End Strand Distance 0 chr1 1 4238 + 173555 1 chr1 1 4238 + 1535335 2 chr1 519643 529390 - 339376 3 chr1 519643 529390 - 1010183 4 chr1 9778855 9788814 - 8236808 5 chr1 9778855 9788814 - 9598588 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2s183eoo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2s183eoo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 7 chr2 8 265 - 5624841 8 chr2 8 265 - 5624841 9 chr2 8 265 - 5624841 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8 | 265 | a | 0 | ... | | chr1 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | | chr2 | 8 | 265 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 2 chr2 8 265 - 5624841 3 chr2 8 265 - 5624841 4 chr2 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 df2 Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 7 chr2 8 265 - 5624841 8 chr2 8 265 - 5624841 9 chr2 8 265 - 5624841 Actual Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 2 chr2 8 265 - 5624841 3 chr2 8 265 - 5624841 4 chr2 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 Expected Chromosome Start End Strand Distance 0 chr1 8 265 - 5624841 1 chr1 8 265 - 5624841 2 chr2 8 265 - 5624841 3 chr2 8 265 - 5624841 4 chr2 8 265 - 5624841 5 chr2 8 265 - 5624841 6 chr2 8 265 - 5624841 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb1ji0sbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb1ji0sbx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 4 chr7 519643 529390 - 5095716 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 293 | a | 0 | ... | | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5629342 | a | 0 | ... | | chr7 | 519643 | 529390 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 5 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 4 chr7 5625105 5629342 - 5095716 2 chr7 5625105 5635064 + 5095716 3 chr7 5625105 5635064 + 5095716 df2 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 4 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 Actual Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Expected Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4y3ilshz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4y3ilshz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 4 chr7 519643 529390 - 5095716 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 293 | a | 0 | ... | | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5629342 | a | 0 | ... | | chr7 | 519643 | 529390 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 5 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 4 chr7 5625105 5629342 - 5095716 2 chr7 5625105 5635064 + 5095716 3 chr7 5625105 5635064 + 5095716 df2 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 4 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 Actual Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Expected Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk930trl0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk930trl0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 4 chr7 519643 529390 - 5095716 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 293 | a | 0 | ... | | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5635064 | a | 0 | ... | | chr7 | 5625105 | 5629342 | a | 0 | ... | | chr7 | 519643 | 529390 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 5 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 4 chr7 5625105 5629342 - 5095716 2 chr7 5625105 5635064 + 5095716 3 chr7 5625105 5635064 + 5095716 df2 Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 4 chr7 519643 529390 - 5095716 1 chr1 5625105 5625302 - 5624813 5 chr7 5625105 5629342 - 5095716 6 chr7 5625105 5635064 + 5095716 7 chr7 5625105 5635064 + 5095716 Actual Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Expected Chromosome Start End Strand Distance 0 chr1 4 293 - 5624813 1 chr1 5625105 5625302 - 5624813 2 chr7 519643 529390 - 5095716 3 chr7 5625105 5629342 - 5095716 4 chr7 5625105 5635064 + 5095716 5 chr7 5625105 5635064 + 5095716 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2w0cz04u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2w0cz04u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 5625105 5625302 - 5619510 2 chr1 5625105 5625302 - 5623070 3 chr2 5625105 5632257 - 5625096 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr1 | 5625105 | 5625302 | a | 0 | ... | | chr2 | 5625105 | 5632257 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5625105 5625302 - 5619510 1 chr1 5625105 5625302 - 5623070 2 chr2 5625105 5632257 - 5625096 df2 Chromosome Start End Strand Distance 1 chr1 5625105 5625302 - 5619510 2 chr1 5625105 5625302 - 5623070 3 chr2 5625105 5632257 - 5625096 Actual Chromosome Start End Strand Distance 0 chr1 5625105 5625302 - 5619510 1 chr1 5625105 5625302 - 5623070 2 chr2 5625105 5632257 - 5625096 Expected Chromosome Start End Strand Distance 0 chr1 5625105 5625302 - 5619510 1 chr1 5625105 5625302 - 5623070 2 chr2 5625105 5632257 - 5625096 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn8723zgi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn8723zgi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3747226 - 454904 1 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 4 chr1 4158022 4162240 - 875230 5 chr1 4158022 4162240 - 999525 6 chr1 4802045 4807630 + 354135 7 chr1 4802045 4807630 + 1519253 8 chr1 7165218 7172547 + 796551 9 chr1 7165218 7172547 + 1482859 10 chr1 7312411 7316991 - 652107 11 chr1 7312411 7316991 - 1338415 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4807630 | a | 0 | ... | | chr1 | 4802045 | 4807630 | a | 0 | ... | | chr1 | 3779696 | 3782240 | a | 0 | ... | | chr1 | 3779696 | 3782240 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7316991 | a | 0 | ... | | chr1 | 7312411 | 7316991 | a | 0 | ... | | chr1 | 3737696 | 3747226 | a | 0 | ... | | chr1 | 3737696 | 3747226 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3747226 - 454904 11 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 6 chr1 4158022 4162240 - 875230 7 chr1 4158022 4162240 - 999525 0 chr1 4802045 4807630 + 354135 1 chr1 4802045 4807630 + 1519253 4 chr1 7165218 7172547 + 796551 5 chr1 7165218 7172547 + 1482859 8 chr1 7312411 7316991 - 652107 9 chr1 7312411 7316991 - 1338415 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3747226 - 454904 1 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 4 chr1 4158022 4162240 - 875230 5 chr1 4158022 4162240 - 999525 6 chr1 4802045 4807630 + 354135 7 chr1 4802045 4807630 + 1519253 8 chr1 7165218 7172547 + 796551 9 chr1 7165218 7172547 + 1482859 10 chr1 7312411 7316991 - 652107 11 chr1 7312411 7316991 - 1338415 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3747226 - 454904 1 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 4 chr1 4158022 4162240 - 875230 5 chr1 4158022 4162240 - 999525 6 chr1 4802045 4807630 + 354135 7 chr1 4802045 4807630 + 1519253 8 chr1 7165218 7172547 + 796551 9 chr1 7165218 7172547 + 1482859 10 chr1 7312411 7316991 - 652107 11 chr1 7312411 7316991 - 1338415 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3747226 - 454904 1 chr1 3737696 3747226 - 1414539 2 chr1 3779696 3782240 + 496904 3 chr1 3779696 3782240 + 1379525 4 chr1 4158022 4162240 - 875230 5 chr1 4158022 4162240 - 999525 6 chr1 4802045 4807630 + 354135 7 chr1 4802045 4807630 + 1519253 8 chr1 7165218 7172547 + 796551 9 chr1 7165218 7172547 + 1482859 10 chr1 7312411 7316991 - 652107 11 chr1 7312411 7316991 - 1338415 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpico87kom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpico87kom/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 454904 11 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 6 chr1 4158022 4161889 - 875230 7 chr1 4158022 4161889 - 999876 0 chr1 4802045 4802055 + 359710 1 chr1 4802045 4802055 + 1519253 4 chr1 7165218 7166229 + 802869 5 chr1 7165218 7166229 + 1489177 8 chr1 7312411 7313422 - 655676 9 chr1 7312411 7313422 - 1341984 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnn1kr4hh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnn1kr4hh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 454904 11 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 6 chr1 4158022 4161889 - 875230 7 chr1 4158022 4161889 - 999876 0 chr1 4802045 4802055 + 359710 1 chr1 4802045 4802055 + 1519253 4 chr1 7165218 7166229 + 802869 5 chr1 7165218 7166229 + 1489177 8 chr1 7312411 7313422 - 655676 9 chr1 7312411 7313422 - 1341984 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 454904 1 chr1 3737696 3741067 - 1420698 2 chr1 3779696 3780465 + 496904 3 chr1 3779696 3780465 + 1381300 4 chr1 4158022 4161889 - 875230 5 chr1 4158022 4161889 - 999876 6 chr1 4802045 4802055 + 359710 7 chr1 4802045 4802055 + 1519253 8 chr1 7165218 7166229 + 802869 9 chr1 7165218 7166229 + 1489177 10 chr1 7312411 7313422 - 655676 11 chr1 7312411 7313422 - 1341984 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdu_eb19b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdu_eb19b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 2378209 1 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 4 chr1 4158022 4161889 - 2798535 5 chr1 4158022 4161889 - 4092484 6 chr1 4802045 4802055 + 3442558 7 chr1 4802045 4802055 + 4736507 8 chr1 7165218 7166229 + 5805731 9 chr1 7165218 7166229 + 7099680 10 chr1 7312411 7313422 - 5952924 11 chr1 7312411 7313422 - 7246873 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 2378209 11 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 6 chr1 4158022 4161889 - 2798535 7 chr1 4158022 4161889 - 4092484 0 chr1 4802045 4802055 + 3442558 1 chr1 4802045 4802055 + 4736507 4 chr1 7165218 7166229 + 5805731 5 chr1 7165218 7166229 + 7099680 8 chr1 7312411 7313422 - 5952924 9 chr1 7312411 7313422 - 7246873 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 2378209 1 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 4 chr1 4158022 4161889 - 2798535 5 chr1 4158022 4161889 - 4092484 6 chr1 4802045 4802055 + 3442558 7 chr1 4802045 4802055 + 4736507 8 chr1 7165218 7166229 + 5805731 9 chr1 7165218 7166229 + 7099680 10 chr1 7312411 7313422 - 5952924 11 chr1 7312411 7313422 - 7246873 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 2378209 1 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 4 chr1 4158022 4161889 - 2798535 5 chr1 4158022 4161889 - 4092484 6 chr1 4802045 4802055 + 3442558 7 chr1 4802045 4802055 + 4736507 8 chr1 7165218 7166229 + 5805731 9 chr1 7165218 7166229 + 7099680 10 chr1 7312411 7313422 - 5952924 11 chr1 7312411 7313422 - 7246873 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 2378209 1 chr1 3737696 3741067 - 3672158 2 chr1 3779696 3780465 + 2420209 3 chr1 3779696 3780465 + 3714158 4 chr1 4158022 4161889 - 2798535 5 chr1 4158022 4161889 - 4092484 6 chr1 4802045 4802055 + 3442558 7 chr1 4802045 4802055 + 4736507 8 chr1 7165218 7166229 + 5805731 9 chr1 7165218 7166229 + 7099680 10 chr1 7312411 7313422 - 5952924 11 chr1 7312411 7313422 - 7246873 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp28icy_lf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28icy_lf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 38630 1 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 4 chr1 4158022 4161889 - 377558 5 chr1 4158022 4161889 - 416956 6 chr1 4802045 4802055 + 640157 7 chr1 4802045 4802055 + 1021581 8 chr1 7165218 7166229 + 146183 9 chr1 7165218 7166229 + 2363164 10 chr1 7312411 7313422 - 146183 11 chr1 7312411 7313422 - 2510357 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 7312411 | 7313422 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 38630 11 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 6 chr1 4158022 4161889 - 377558 7 chr1 4158022 4161889 - 416956 0 chr1 4802045 4802055 + 640157 1 chr1 4802045 4802055 + 1021581 4 chr1 7165218 7166229 + 146183 5 chr1 7165218 7166229 + 2363164 8 chr1 7312411 7313422 - 146183 9 chr1 7312411 7313422 - 2510357 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 38630 1 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 4 chr1 4158022 4161889 - 377558 5 chr1 4158022 4161889 - 416956 6 chr1 4802045 4802055 + 640157 7 chr1 4802045 4802055 + 1021581 8 chr1 7165218 7166229 + 146183 9 chr1 7165218 7166229 + 2363164 10 chr1 7312411 7313422 - 146183 11 chr1 7312411 7313422 - 2510357 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 38630 1 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 4 chr1 4158022 4161889 - 377558 5 chr1 4158022 4161889 - 416956 6 chr1 4802045 4802055 + 640157 7 chr1 4802045 4802055 + 1021581 8 chr1 7165218 7166229 + 146183 9 chr1 7165218 7166229 + 2363164 10 chr1 7312411 7313422 - 146183 11 chr1 7312411 7313422 - 2510357 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 38630 1 chr1 3737696 3741067 - 416956 2 chr1 3779696 3780465 + 38630 3 chr1 3779696 3780465 + 377558 4 chr1 4158022 4161889 - 377558 5 chr1 4158022 4161889 - 416956 6 chr1 4802045 4802055 + 640157 7 chr1 4802045 4802055 + 1021581 8 chr1 7165218 7166229 + 146183 9 chr1 7165218 7166229 + 2363164 10 chr1 7312411 7313422 - 146183 11 chr1 7312411 7313422 - 2510357 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpasp69p10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasp69p10/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 3737353 1 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 6 chr1 4802045 4802055 + 2793436 7 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 10 chr1 7312411 7313422 - 282069 11 chr1 7312411 7313422 - 7312068 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 4802045 | 4802055 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | chr1 | 3779696 | 3780465 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7165218 | 7166229 | a | 0 | ... | | chr1 | 7165218 | 7166229 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | | chr1 | 3737696 | 3741067 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3737696 3741067 - 3737353 11 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 0 chr1 4802045 4802055 + 2793436 1 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 6 chr1 7312411 7313422 - 282069 7 chr1 7312411 7313422 - 7312068 df2 Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 3737353 1 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 6 chr1 4802045 4802055 + 2793436 7 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 10 chr1 7312411 7313422 - 282069 11 chr1 7312411 7313422 - 7312068 Actual Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 3737353 1 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 6 chr1 4802045 4802055 + 2793436 7 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 10 chr1 7312411 7313422 - 282069 11 chr1 7312411 7313422 - 7312068 Expected Chromosome Start End Strand Distance 0 chr1 3737696 3741067 - 3737353 1 chr1 3737696 3741067 - 3854424 2 chr1 3779696 3780465 + 3779353 3 chr1 3779696 3780465 + 3815026 4 chr1 4158022 4161889 - 3433602 5 chr1 4158022 4161889 - 4157679 6 chr1 4802045 4802055 + 2793436 7 chr1 4802045 4802055 + 4801702 8 chr1 7165218 7166229 - 429262 9 chr1 7165218 7166229 - 7164875 10 chr1 7312411 7313422 - 282069 11 chr1 7312411 7313422 - 7312068 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp37v968ac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37v968ac/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_dftiyqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dftiyqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8613393 | 8613655 | a | 0 | ... | | chr1 | 8613393 | 8613655 | a | 0 | ... | | chr4 | 1475361 | 1475623 | a | 0 | ... | | chr4 | 1475361 | 1475623 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 df2 Chromosome Start End Strand Distance 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 Actual Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 Expected Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 3675072 1 chr1 8613393 8613655 - 3772311 2 chr4 1475361 1475623 + 2002713 3 chr4 1475361 1475623 + 6146671 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghy5zeaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghy5zeaa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8613393 | 8613655 | a | 0 | ... | | chr1 | 8613393 | 8613655 | a | 0 | ... | | chr4 | 1475361 | 1475623 | a | 0 | ... | | chr4 | 1475361 | 1475623 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 df2 Chromosome Start End Strand Distance 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 Actual Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 Expected Chromosome Start End Strand Distance 0 chr1 8613393 8613655 - 8603404 1 chr1 8613393 8613655 - 8610887 2 chr4 1475361 1475623 + 1475100 3 chr4 1475361 1475623 + 1475104 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx7tngfrc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7tngfrc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprf9t7syy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprf9t7syy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdh6mjtxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdh6mjtxo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_tyb_zs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_tyb_zs5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpynhrnxl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpynhrnxl6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi9aqqn84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi9aqqn84/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 1 chr1 5369850 5372723 + 2649239 2 chr1 5496784 5501287 + 2776173 3 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4512657 | 4519206 | a | 0 | ... | | chr1 | 6679183 | 6685420 | a | 0 | ... | | chr1 | 5369850 | 5372723 | a | 0 | ... | | chr1 | 5496784 | 5501287 | a | 0 | ... | | chr1 | 6945544 | 6951253 | a | 0 | ... | | chr1 | 7707968 | 7709268 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 2 chr1 5369850 5372723 + 2649239 3 chr1 5496784 5501287 + 2776173 1 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 df2 Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 1 chr1 5369850 5372723 + 2649239 2 chr1 5496784 5501287 + 2776173 3 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 Actual Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 1 chr1 5369850 5372723 + 2649239 2 chr1 5496784 5501287 + 2776173 3 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 Expected Chromosome Start End Strand Distance 0 chr1 4512657 4519206 + 1792046 1 chr1 5369850 5372723 + 2649239 2 chr1 5496784 5501287 + 2776173 3 chr1 6679183 6685420 + 3958572 4 chr1 6945544 6951253 - 4224933 5 chr1 7707968 7709268 - 4987357 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjqyv3kwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqyv3kwa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 3 2 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65272 6 chr1 65537 65794 - 65519 7 chr1 5369850 5369960 - 5304304 8 chr1 5369850 5369960 - 5369585 9 chr1 6679183 6679293 - 6613637 10 chr1 6679183 6679293 - 6678918 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 111 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 7 chr1 6 116 - 3 8 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 1 chr1 65537 65794 - 65272 2 chr1 65537 65794 - 65519 9 chr1 5369850 5369960 - 5304304 10 chr1 5369850 5369960 - 5369585 5 chr1 6679183 6679293 - 6613637 6 chr1 6679183 6679293 - 6678918 df2 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 3 2 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65272 6 chr1 65537 65794 - 65519 7 chr1 5369850 5369960 - 5304304 8 chr1 5369850 5369960 - 5369585 9 chr1 6679183 6679293 - 6613637 10 chr1 6679183 6679293 - 6678918 Actual Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 3 2 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65272 6 chr1 65537 65794 - 65519 7 chr1 5369850 5369960 - 5304304 8 chr1 5369850 5369960 - 5369585 9 chr1 6679183 6679293 - 6613637 10 chr1 6679183 6679293 - 6678918 Expected Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 3 2 chr1 6 116 - 65422 3 chr1 7 117 - 4 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65272 6 chr1 65537 65794 - 65519 7 chr1 5369850 5369960 - 5304304 8 chr1 5369850 5369960 - 5369585 9 chr1 6679183 6679293 - 6613637 10 chr1 6679183 6679293 - 6678918 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7q63jzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7q63jzi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65794 - 65280 4 chr1 5369850 5369960 - 5369593 5 chr1 6679183 6679293 - 6678926 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 6679183 | 6679293 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 2 chr1 5369850 5369960 - 5369593 1 chr1 6679183 6679293 - 6678926 df2 Chromosome Start End Strand Distance 3 chr1 65537 65794 - 65280 4 chr1 5369850 5369960 - 5369593 5 chr1 6679183 6679293 - 6678926 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 1 chr1 5369850 5369960 - 5369593 2 chr1 6679183 6679293 - 6678926 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 1 chr1 5369850 5369960 - 5369593 2 chr1 6679183 6679293 - 6678926 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwfanea8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwfanea8_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65794 - 65280 4 chr1 5369850 5369960 - 5369593 5 chr1 6679183 6679293 - 6678926 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 6679183 | 6679293 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 2 chr1 5369850 5369960 - 5369593 1 chr1 6679183 6679293 - 6678926 df2 Chromosome Start End Strand Distance 3 chr1 65537 65794 - 65280 4 chr1 5369850 5369960 - 5369593 5 chr1 6679183 6679293 - 6678926 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 1 chr1 5369850 5369960 - 5369593 2 chr1 6679183 6679293 - 6678926 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65280 1 chr1 5369850 5369960 - 5369593 2 chr1 6679183 6679293 - 6678926 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_yjxk5n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_yjxk5n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 2 chr1 6 116 - 65422 3 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 6 chr1 65537 65794 - 65421 7 chr1 65537 65794 - 65422 8 chr1 5369850 5369960 - 1309224 9 chr1 5369850 5369960 - 5304057 10 chr1 6679183 6679293 - 1309224 11 chr1 6679183 6679293 - 6613390 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 111 | a | 0 | ... | | chr1 | 1 | 111 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 8 chr1 6 116 - 65422 9 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 2 chr1 65537 65794 - 65421 3 chr1 65537 65794 - 65422 10 chr1 5369850 5369960 - 1309224 11 chr1 5369850 5369960 - 5304057 6 chr1 6679183 6679293 - 1309224 7 chr1 6679183 6679293 - 6613390 df2 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 2 chr1 6 116 - 65422 3 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 6 chr1 65537 65794 - 65421 7 chr1 65537 65794 - 65422 8 chr1 5369850 5369960 - 1309224 9 chr1 5369850 5369960 - 5304057 10 chr1 6679183 6679293 - 1309224 11 chr1 6679183 6679293 - 6613390 Actual Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 2 chr1 6 116 - 65422 3 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 6 chr1 65537 65794 - 65421 7 chr1 65537 65794 - 65422 8 chr1 5369850 5369960 - 1309224 9 chr1 5369850 5369960 - 5304057 10 chr1 6679183 6679293 - 1309224 11 chr1 6679183 6679293 - 6613390 Expected Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 1 111 - 5369740 2 chr1 6 116 - 65422 3 chr1 6 116 - 5369735 4 chr1 7 117 - 65421 5 chr1 7 117 - 5369734 6 chr1 65537 65794 - 65421 7 chr1 65537 65794 - 65422 8 chr1 5369850 5369960 - 1309224 9 chr1 5369850 5369960 - 5304057 10 chr1 6679183 6679293 - 1309224 11 chr1 6679183 6679293 - 6613390 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd0064qou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0064qou/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 6 116 - 1 2 chr1 7 117 - 1 3 chr1 7 117 - 2 4 chr1 65537 65794 - 55830 5 chr1 65537 65794 - 60945 6 chr1 5369850 5369960 - 5360143 7 chr1 5369850 5369960 - 5365258 8 chr1 6679183 6679293 - 6669476 9 chr1 6679183 6679293 - 6674591 11 chr3 9 119 - 6 12 chr9 65537 65647 - 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6679183 | 6679293 | a | 0 | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 6 116 - 1 2 chr1 7 117 - 1 3 chr1 7 117 - 2 9 chr3 9 119 - 6 10 chr9 65537 65647 - 65280 0 chr1 65537 65794 - 55830 1 chr1 65537 65794 - 60945 7 chr1 5369850 5369960 - 5360143 8 chr1 5369850 5369960 - 5365258 4 chr1 6679183 6679293 - 6669476 5 chr1 6679183 6679293 - 6674591 df2 Chromosome Start End Strand Distance 1 chr1 6 116 - 1 2 chr1 7 117 - 1 3 chr1 7 117 - 2 11 chr3 9 119 - 6 12 chr9 65537 65647 - 65280 4 chr1 65537 65794 - 55830 5 chr1 65537 65794 - 60945 6 chr1 5369850 5369960 - 5360143 7 chr1 5369850 5369960 - 5365258 8 chr1 6679183 6679293 - 6669476 9 chr1 6679183 6679293 - 6674591 Actual Chromosome Start End Strand Distance 0 chr1 6 116 - 1 1 chr1 7 117 - 1 2 chr1 7 117 - 2 3 chr1 65537 65794 - 55830 4 chr1 65537 65794 - 60945 5 chr1 5369850 5369960 - 5360143 6 chr1 5369850 5369960 - 5365258 7 chr1 6679183 6679293 - 6669476 8 chr1 6679183 6679293 - 6674591 9 chr3 9 119 - 6 10 chr9 65537 65647 - 65280 Expected Chromosome Start End Strand Distance 0 chr1 6 116 - 1 1 chr1 7 117 - 1 2 chr1 7 117 - 2 3 chr1 65537 65794 - 55830 4 chr1 65537 65794 - 60945 5 chr1 5369850 5369960 - 5360143 6 chr1 5369850 5369960 - 5365258 7 chr1 6679183 6679293 - 6669476 8 chr1 6679183 6679293 - 6674591 9 chr3 9 119 - 6 10 chr9 65537 65647 - 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmiw_38n5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmiw_38n5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 5 2 chr1 6 116 - 65422 3 chr1 7 117 - 6 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65536 6 chr1 5369850 5369960 - 5304307 7 chr1 5369850 5369960 - 5369849 8 chr1 6679183 6679293 - 6613640 9 chr1 6679183 6679293 - 6679182 11 chr3 9 119 - 8 12 chr9 65537 65647 - 65536 13 chrM 7 117 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 111 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | chr1 | 7 | 117 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 6 | 116 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | | chr1 | 5369850 | 5369960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 6 chr1 6 116 - 5 7 chr1 6 116 - 65422 2 chr1 7 117 - 6 12 chrM 7 117 - 6 3 chr1 7 117 - 65421 10 chr3 9 119 - 8 11 chr9 65537 65647 - 65536 1 chr1 65537 65794 - 65536 8 chr1 5369850 5369960 - 5304307 9 chr1 5369850 5369960 - 5369849 4 chr1 6679183 6679293 - 6613640 5 chr1 6679183 6679293 - 6679182 df2 Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 5 2 chr1 6 116 - 65422 3 chr1 7 117 - 6 13 chrM 7 117 - 6 4 chr1 7 117 - 65421 11 chr3 9 119 - 8 12 chr9 65537 65647 - 65536 5 chr1 65537 65794 - 65536 6 chr1 5369850 5369960 - 5304307 7 chr1 5369850 5369960 - 5369849 8 chr1 6679183 6679293 - 6613640 9 chr1 6679183 6679293 - 6679182 Actual Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 5 2 chr1 6 116 - 65422 3 chr1 7 117 - 6 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65536 6 chr1 5369850 5369960 - 5304307 7 chr1 5369850 5369960 - 5369849 8 chr1 6679183 6679293 - 6613640 9 chr1 6679183 6679293 - 6679182 10 chr3 9 119 - 8 11 chr9 65537 65647 - 65536 12 chrM 7 117 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 111 - 65427 1 chr1 6 116 - 5 2 chr1 6 116 - 65422 3 chr1 7 117 - 6 4 chr1 7 117 - 65421 5 chr1 65537 65794 - 65536 6 chr1 5369850 5369960 - 5304307 7 chr1 5369850 5369960 - 5369849 8 chr1 6679183 6679293 - 6613640 9 chr1 6679183 6679293 - 6679182 10 chr3 9 119 - 8 11 chr9 65537 65647 - 65536 12 chrM 7 117 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbtrw3hi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbtrw3hi6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 460608 - 2130996 1 chr1 450608 460608 - 9088653 2 chr1 1644931 1654931 + 936673 3 chr1 1644931 1654931 + 7894330 4 chr1 4588101 4598101 - 1993499 5 chr1 4588101 4598101 - 4951160 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 450608 460608 - 2130996 5 chr1 450608 460608 - 9088653 0 chr1 1644931 1654931 + 936673 1 chr1 1644931 1654931 + 7894330 2 chr1 4588101 4598101 - 1993499 3 chr1 4588101 4598101 - 4951160 df2 Chromosome Start End Strand Distance 0 chr1 450608 460608 - 2130996 1 chr1 450608 460608 - 9088653 2 chr1 1644931 1654931 + 936673 3 chr1 1644931 1654931 + 7894330 4 chr1 4588101 4598101 - 1993499 5 chr1 4588101 4598101 - 4951160 Actual Chromosome Start End Strand Distance 0 chr1 450608 460608 - 2130996 1 chr1 450608 460608 - 9088653 2 chr1 1644931 1654931 + 936673 3 chr1 1644931 1654931 + 7894330 4 chr1 4588101 4598101 - 1993499 5 chr1 4588101 4598101 - 4951160 Expected Chromosome Start End Strand Distance 0 chr1 450608 460608 - 2130996 1 chr1 450608 460608 - 9088653 2 chr1 1644931 1654931 + 936673 3 chr1 1644931 1654931 + 7894330 4 chr1 4588101 4598101 - 1993499 5 chr1 4588101 4598101 - 4951160 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvk9n4ff2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvk9n4ff2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 460608 - 444910 0 chr1 1644931 1654931 + 1639233 1 chr1 4588101 4598101 - 4582403 df2 Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Expected Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4mm4_07w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mm4_07w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 460608 - 444910 0 chr1 1644931 1654931 + 1639233 1 chr1 4588101 4598101 - 4582403 df2 Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Expected Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptlr2xc88/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlr2xc88/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1644931 | 1654931 | a | 0 | ... | | chr1 | 4588101 | 4598101 | a | 0 | ... | | chr1 | 450608 | 460608 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 460608 - 444910 0 chr1 1644931 1654931 + 1639233 1 chr1 4588101 4598101 - 4582403 df2 Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Expected Chromosome Start End Strand Distance 0 chr1 450608 460608 - 444910 1 chr1 1644931 1654931 + 1639233 2 chr1 4588101 4598101 - 4582403 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7kbw3z5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7kbw3z5w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4588101 | 4588104 | a | 0 | ... | | chr1 | 4588101 | 4588104 | a | 0 | ... | | chr1 | 450608 | 450865 | a | 0 | ... | | chr1 | 450608 | 450865 | a | 0 | ... | | chr1 | 1644931 | 1644933 | a | 0 | ... | | chr1 | 1644931 | 1644933 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 450865 - 450597 3 chr1 450608 450865 - 2158496 4 chr1 1644931 1644933 - 964428 5 chr1 1644931 1644933 - 1644920 0 chr1 4588101 4588104 - 1978741 1 chr1 4588101 4588104 - 4588090 df2 Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Actual Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Expected Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcxiyvtrs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxiyvtrs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4588101 | 4588104 | a | 0 | ... | | chr1 | 4588101 | 4588104 | a | 0 | ... | | chr1 | 450608 | 450865 | a | 0 | ... | | chr1 | 450608 | 450865 | a | 0 | ... | | chr1 | 1644931 | 1644933 | a | 0 | ... | | chr1 | 1644931 | 1644933 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 450608 450865 - 450597 3 chr1 450608 450865 - 2158496 4 chr1 1644931 1644933 - 964428 5 chr1 1644931 1644933 - 1644920 0 chr1 4588101 4588104 - 1978741 1 chr1 4588101 4588104 - 4588090 df2 Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Actual Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Expected Chromosome Start End Strand Distance 0 chr1 450608 450865 - 450597 1 chr1 450608 450865 - 2158496 2 chr1 1644931 1644933 - 964428 3 chr1 1644931 1644933 - 1644920 4 chr1 4588101 4588104 - 1978741 5 chr1 4588101 4588104 - 4588090 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvthhnmg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvthhnmg_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr2 1 3 - 9 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 3 - 9 df2 Chromosome Start End Strand Distance 3 chr2 1 3 - 9 Actual Chromosome Start End Strand Distance 0 chr2 1 3 - 9 Expected Chromosome Start End Strand Distance 0 chr2 1 3 - 9 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxcrcu0zb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcrcu0zb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 6273276 1 chr1 1585214 1587914 - 8082640 2 chr1 2087956 2095084 - 5766106 3 chr1 2087956 2095084 - 7575470 4 chr1 7414117 7423198 - 437992 5 chr1 7414117 7423198 - 2247356 6 chr19 3302345 3308284 - 1772474 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2087956 | 2095084 | a | 0 | ... | | chr1 | 2087956 | 2095084 | a | 0 | ... | | chr1 | 7414117 | 7423198 | a | 0 | ... | | chr1 | 7414117 | 7423198 | a | 0 | ... | | chr1 | 1585214 | 1587914 | a | 0 | ... | | chr1 | 1585214 | 1587914 | a | 0 | ... | | chr19 | 3302345 | 3308284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1585214 1587914 - 6273276 5 chr1 1585214 1587914 - 8082640 0 chr1 2087956 2095084 - 5766106 1 chr1 2087956 2095084 - 7575470 6 chr19 3302345 3308284 - 1772474 2 chr1 7414117 7423198 - 437992 3 chr1 7414117 7423198 - 2247356 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 6273276 1 chr1 1585214 1587914 - 8082640 2 chr1 2087956 2095084 - 5766106 3 chr1 2087956 2095084 - 7575470 6 chr19 3302345 3308284 - 1772474 4 chr1 7414117 7423198 - 437992 5 chr1 7414117 7423198 - 2247356 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 6273276 1 chr1 1585214 1587914 - 8082640 2 chr1 2087956 2095084 - 5766106 3 chr1 2087956 2095084 - 7575470 4 chr1 7414117 7423198 - 437992 5 chr1 7414117 7423198 - 2247356 6 chr19 3302345 3308284 - 1772474 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 6273276 1 chr1 1585214 1587914 - 8082640 2 chr1 2087956 2095084 - 5766106 3 chr1 2087956 2095084 - 7575470 4 chr1 7414117 7423198 - 437992 5 chr1 7414117 7423198 - 2247356 6 chr19 3302345 3308284 - 1772474 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6u_zqlx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6u_zqlx0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2087956 | 2095084 | a | 0 | ... | | chr1 | 7414117 | 7423198 | a | 0 | ... | | chr1 | 1585214 | 1587914 | a | 0 | ... | | chr19 | 3302345 | 3308284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1585214 1587914 - 1584952 0 chr1 2087956 2095084 - 2087694 3 chr19 3302345 3308284 - 3302083 1 chr1 7414117 7423198 - 7413855 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 3 chr19 3302345 3308284 - 3302083 2 chr1 7414117 7423198 - 7413855 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjh5d42qj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh5d42qj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2087956 | 2095084 | a | 0 | ... | | chr1 | 7414117 | 7423198 | a | 0 | ... | | chr1 | 1585214 | 1587914 | a | 0 | ... | | chr19 | 3302345 | 3308284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1585214 1587914 - 1584952 0 chr1 2087956 2095084 - 2087694 3 chr19 3302345 3308284 - 3302083 1 chr1 7414117 7423198 - 7413855 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 3 chr19 3302345 3308284 - 3302083 2 chr1 7414117 7423198 - 7413855 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1587914 - 1584952 1 chr1 2087956 2095084 - 2087694 2 chr1 7414117 7423198 - 7413855 3 chr19 3302345 3308284 - 3302083 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1upyokfo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1upyokfo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr19 3302345 3308284 - 3302083 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr19 | 3302345 | 3308284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr19 3302345 3308284 - 3302083 df2 Chromosome Start End Strand Distance 3 chr19 3302345 3308284 - 3302083 Actual Chromosome Start End Strand Distance 0 chr19 3302345 3308284 - 3302083 Expected Chromosome Start End Strand Distance 0 chr19 3302345 3308284 - 3302083 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnsj8sg_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnsj8sg_6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7414117 | 7414219 | a | 0 | ... | | chr1 | 1585214 | 1585215 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1585214 1585215 - 1519631 0 chr1 7414117 7414219 - 7348534 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk2ut607w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2ut607w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7414117 | 7414219 | a | 0 | ... | | chr1 | 1585214 | 1585215 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1585214 1585215 - 1519631 0 chr1 7414117 7414219 - 7348534 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1585215 - 1519631 1 chr1 7414117 7414219 - 7348534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgtxn_hkj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgtxn_hkj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1585214 1585215 + 1519631 1 chr1 7414117 7414219 + 7348534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7414117 | 7414219 | a | 0 | ... | | chr1 | 1585214 | 1585215 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1585214 1585215 + 1519631 0 chr1 7414117 7414219 + 7348534 df2 Chromosome Start End Strand Distance 0 chr1 1585214 1585215 + 1519631 1 chr1 7414117 7414219 + 7348534 Actual Chromosome Start End Strand Distance 0 chr1 1585214 1585215 + 1519631 1 chr1 7414117 7414219 + 7348534 Expected Chromosome Start End Strand Distance 0 chr1 1585214 1585215 + 1519631 1 chr1 7414117 7414219 + 7348534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7p518_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7p518_l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 159458 1 chr1 3523727 3530748 - 1108129 2 chr1 6765373 6765374 - 191412 3 chr1 6765373 6765374 - 192832 4 chr1 6765373 6767936 + 191412 5 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 10 chr1 6765373 6775211 + 191412 11 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6765373 | 6767936 | a | 0 | ... | | chr1 | 6765373 | 6767936 | a | 0 | ... | | chr1 | 6765373 | 6775211 | a | 0 | ... | | chr1 | 6765373 | 6775211 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6765373 | 6773593 | a | 0 | ... | | chr1 | 6765373 | 6773593 | a | 0 | ... | | chr1 | 3523727 | 3530748 | a | 0 | ... | | chr1 | 3523727 | 3530748 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 3523727 3530748 - 159458 11 chr1 3523727 3530748 - 1108129 4 chr1 6765373 6765374 - 191412 5 chr1 6765373 6765374 - 192832 0 chr1 6765373 6767936 + 191412 1 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 2 chr1 6765373 6775211 + 191412 3 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 df2 Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 159458 1 chr1 3523727 3530748 - 1108129 2 chr1 6765373 6765374 - 191412 3 chr1 6765373 6765374 - 192832 4 chr1 6765373 6767936 + 191412 5 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 10 chr1 6765373 6775211 + 191412 11 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 Actual Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 159458 1 chr1 3523727 3530748 - 1108129 2 chr1 6765373 6765374 - 191412 3 chr1 6765373 6765374 - 192832 4 chr1 6765373 6767936 + 191412 5 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 10 chr1 6765373 6775211 + 191412 11 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 Expected Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 159458 1 chr1 3523727 3530748 - 1108129 2 chr1 6765373 6765374 - 191412 3 chr1 6765373 6765374 - 192832 4 chr1 6765373 6767936 + 191412 5 chr1 6765373 6767936 + 192832 6 chr1 6765373 6771834 - 191412 7 chr1 6765373 6771834 - 192832 8 chr1 6765373 6773593 - 191412 9 chr1 6765373 6773593 - 192832 10 chr1 6765373 6775211 + 191412 11 chr1 6765373 6775211 + 192832 12 chr10 8778908 8784751 - 8228448 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnf0embpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnf0embpi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 5 chr1 6765373 6775211 + 3234626 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6765373 | 6767936 | a | 0 | ... | | chr1 | 6765373 | 6775211 | a | 0 | ... | | chr1 | 6765373 | 6765374 | a | 0 | ... | | chr1 | 6765373 | 6771834 | a | 0 | ... | | chr1 | 6765373 | 6773593 | a | 0 | ... | | chr1 | 3523727 | 3530748 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 3523727 3530748 - 3234626 2 chr1 6765373 6765374 - 3234626 0 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 1 chr1 6765373 6775211 + 3234626 df2 Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 5 chr1 6765373 6775211 + 3234626 Actual Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 5 chr1 6765373 6775211 + 3234626 Expected Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 - 3234626 5 chr1 6765373 6775211 + 3234626 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyxgewsan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyxgewsan/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 + 3234626 5 chr1 6765373 6775211 + 3234626 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6765373 | 6767936 | a | 0 | ... | | chr1 | 6765373 | 6773593 | a | 0 | ... | | chr1 | 6765373 | 6775211 | a | 0 | ... | | chr1 | 6765373 | 6765374 | a | 0 | ... | | chr1 | 6765373 | 6771834 | a | 0 | ... | | chr1 | 3523727 | 3530748 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 3523727 3530748 - 3234626 3 chr1 6765373 6765374 - 3234626 0 chr1 6765373 6767936 + 3234626 4 chr1 6765373 6771834 - 3234626 1 chr1 6765373 6773593 + 3234626 2 chr1 6765373 6775211 + 3234626 df2 Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 + 3234626 5 chr1 6765373 6775211 + 3234626 Actual Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 + 3234626 5 chr1 6765373 6775211 + 3234626 Expected Chromosome Start End Strand Distance 0 chr1 3523727 3530748 - 3234626 1 chr1 6765373 6765374 - 3234626 2 chr1 6765373 6767936 + 3234626 3 chr1 6765373 6771834 - 3234626 4 chr1 6765373 6773593 + 3234626 5 chr1 6765373 6775211 + 3234626 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0eog34v_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0eog34v_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 0 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpke0yoxmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpke0yoxmb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 0 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp6yfl9hd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6yfl9hd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65515 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 0 chr1 65537 65794 - 65515 df2 Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65515 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65515 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65515 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppngq285x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppngq285x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65533 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 3 4 - 1 0 chr1 65537 65794 - 65533 df2 Chromosome Start End Strand Distance 3 chr1 3 4 - 1 4 chr1 3 4 - 1 5 chr1 3 4 - 1 6 chr1 3 4 - 1 7 chr1 65537 65794 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65533 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 1 1 chr1 3 4 - 1 2 chr1 3 4 - 1 3 chr1 3 4 - 1 4 chr1 65537 65794 - 65533 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm5iduuwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm5iduuwd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 451624 1 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 4 chr1 8594171 8604156 + 731414 5 chr1 8594171 8604156 + 1322949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1502864 1507072 - 451624 5 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 0 chr1 8594171 8604156 + 731414 1 chr1 8594171 8604156 + 1322949 df2 Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 451624 1 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 4 chr1 8594171 8604156 + 731414 5 chr1 8594171 8604156 + 1322949 Actual Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 451624 1 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 4 chr1 8594171 8604156 + 731414 5 chr1 8594171 8604156 + 1322949 Expected Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 451624 1 chr1 1502864 1507072 - 1946599 2 chr1 6569069 6577270 - 1085309 3 chr1 6569069 6577270 - 1281576 4 chr1 8594171 8604156 + 731414 5 chr1 8594171 8604156 + 1322949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdo3wxhif/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdo3wxhif/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 5061998 1 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 4 chr1 8594171 8604156 + 2016902 5 chr1 8594171 8604156 + 7087100 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1502864 1507072 - 5061998 5 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 0 chr1 8594171 8604156 + 2016902 1 chr1 8594171 8604156 + 7087100 df2 Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 5061998 1 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 4 chr1 8594171 8604156 + 2016902 5 chr1 8594171 8604156 + 7087100 Actual Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 5061998 1 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 4 chr1 8594171 8604156 + 2016902 5 chr1 8594171 8604156 + 7087100 Expected Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 5061998 1 chr1 1502864 1507072 - 7087100 2 chr1 6569069 6577270 - 2016902 3 chr1 6569069 6577270 - 5061998 4 chr1 8594171 8604156 + 2016902 5 chr1 8594171 8604156 + 7087100 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6znkwv3p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6znkwv3p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 1437326 1 chr1 1502864 1507072 - 1502858 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 4 chr1 8594171 8604156 + 8528633 5 chr1 8594171 8604156 + 8594165 8 chr20 4644978 4649186 - 4644972 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 8594171 | 8604156 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 6569069 | 6577270 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | | chr1 | 1502864 | 1507072 | a | 0 | ... | | chr20 | 4644978 | 4649186 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1502864 1507072 - 1437326 5 chr1 1502864 1507072 - 1502858 6 chr20 4644978 4649186 - 4644972 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 0 chr1 8594171 8604156 + 8528633 1 chr1 8594171 8604156 + 8594165 df2 Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 1437326 1 chr1 1502864 1507072 - 1502858 8 chr20 4644978 4649186 - 4644972 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 4 chr1 8594171 8604156 + 8528633 5 chr1 8594171 8604156 + 8594165 Actual Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 1437326 1 chr1 1502864 1507072 - 1502858 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 4 chr1 8594171 8604156 + 8528633 5 chr1 8594171 8604156 + 8594165 6 chr20 4644978 4649186 - 4644972 Expected Chromosome Start End Strand Distance 0 chr1 1502864 1507072 - 1437326 1 chr1 1502864 1507072 - 1502858 2 chr1 6569069 6577270 - 6503531 3 chr1 6569069 6577270 - 6569063 4 chr1 8594171 8604156 + 8528633 5 chr1 8594171 8604156 + 8594165 6 chr20 4644978 4649186 - 4644972 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyar99xpf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyar99xpf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65532 2 chr1 65537 65539 - 65533 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2 7 - 65531 0 chr1 65537 65539 - 65532 1 chr1 65537 65539 - 65533 df2 Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65532 2 chr1 65537 65539 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65532 2 chr1 65537 65539 - 65533 Expected Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65532 2 chr1 65537 65539 - 65533 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4e715zxo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4e715zxo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65539 | a | 0 | ... | | chr1 | 2 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2 7 - 65531 0 chr1 65537 65539 - 65531 df2 Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 2 7 - 65531 1 chr1 65537 65539 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq3mw8eyb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3mw8eyb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65794 + 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 + 65280 df2 Chromosome Start End Strand Distance 3 chr1 65537 65794 + 65280 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 + 65280 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 + 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8rq4ahr_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8rq4ahr_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfy5nqfs8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfy5nqfs8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl1xumotk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl1xumotk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp957rtx1r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp957rtx1r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgw73l8eo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgw73l8eo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptu4_9tyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptu4_9tyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2y5tuvje/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2y5tuvje/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10 | 16 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 df2 Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 Actual Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 Expected Chromosome Start End Strand Distance 0 chr1 10 16 - 6510133 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuzedo8c6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuzedo8c6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdt3c6xhn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdt3c6xhn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 379353 1 chr1 5631745 5640565 - 2097758 2 chr1 5631745 5640565 - 2098709 3 chr1 8861813 8870991 - 5327826 4 chr1 8861813 8870991 - 5328777 5 chr1 9881162 9884464 - 6347175 6 chr1 9881162 9884464 - 6348126 7 chr1 9881162 9887404 + 6347175 8 chr1 9881162 9887404 + 6348126 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | chr1 | 3144471 | 3146364 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 3144471 3146364 - 379353 2 chr1 5631745 5640565 - 2097758 3 chr1 5631745 5640565 - 2098709 7 chr1 8861813 8870991 - 5327826 8 chr1 8861813 8870991 - 5328777 4 chr1 9881162 9884464 - 6347175 5 chr1 9881162 9884464 - 6348126 0 chr1 9881162 9887404 + 6347175 1 chr1 9881162 9887404 + 6348126 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 379353 1 chr1 5631745 5640565 - 2097758 2 chr1 5631745 5640565 - 2098709 3 chr1 8861813 8870991 - 5327826 4 chr1 8861813 8870991 - 5328777 5 chr1 9881162 9884464 - 6347175 6 chr1 9881162 9884464 - 6348126 7 chr1 9881162 9887404 + 6347175 8 chr1 9881162 9887404 + 6348126 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 379353 1 chr1 5631745 5640565 - 2097758 2 chr1 5631745 5640565 - 2098709 3 chr1 8861813 8870991 - 5327826 4 chr1 8861813 8870991 - 5328777 5 chr1 9881162 9884464 - 6347175 6 chr1 9881162 9884464 - 6348126 7 chr1 9881162 9887404 + 6347175 8 chr1 9881162 9887404 + 6348126 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 379353 1 chr1 5631745 5640565 - 2097758 2 chr1 5631745 5640565 - 2098709 3 chr1 8861813 8870991 - 5327826 4 chr1 8861813 8870991 - 5328777 5 chr1 9881162 9884464 - 6347175 6 chr1 9881162 9884464 - 6348126 7 chr1 9881162 9887404 + 6347175 8 chr1 9881162 9887404 + 6348126 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpln34suwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpln34suwx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 + 1010172 9 chr1 9881162 9887404 + 4240598 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3144471 | 3146364 | a | 0 | ... | | chr1 | 3144471 | 3146364 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 3144471 3146364 - 2485382 7 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 8 chr1 8861813 8870991 - 1010172 9 chr1 8861813 8870991 - 3221249 4 chr1 9881162 9884464 - 1010172 5 chr1 9881162 9884464 - 4240598 0 chr1 9881162 9887404 + 1010172 1 chr1 9881162 9887404 + 4240598 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 + 1010172 9 chr1 9881162 9887404 + 4240598 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 + 1010172 9 chr1 9881162 9887404 + 4240598 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 - 2485382 3 chr1 5631745 5640565 - 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 + 1010172 9 chr1 9881162 9887404 + 4240598 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjra8ep6z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjra8ep6z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 3078934 1 chr1 3144471 3146364 - 3144459 2 chr1 5631745 5640565 + 5566208 3 chr1 5631745 5640565 + 5631733 4 chr1 8861813 8870991 - 8796276 5 chr1 8861813 8870991 - 8861801 6 chr1 9881162 9884464 - 9815625 7 chr1 9881162 9884464 - 9881150 8 chr1 9881162 9887404 - 9815625 9 chr1 9881162 9887404 - 9881150 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 3144471 3146364 - 3078934 5 chr1 3144471 3146364 - 3144459 0 chr1 5631745 5640565 + 5566208 1 chr1 5631745 5640565 + 5631733 8 chr1 8861813 8870991 - 8796276 9 chr1 8861813 8870991 - 8861801 2 chr1 9881162 9884464 - 9815625 3 chr1 9881162 9884464 - 9881150 6 chr1 9881162 9887404 - 9815625 7 chr1 9881162 9887404 - 9881150 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 3078934 1 chr1 3144471 3146364 - 3144459 2 chr1 5631745 5640565 + 5566208 3 chr1 5631745 5640565 + 5631733 4 chr1 8861813 8870991 - 8796276 5 chr1 8861813 8870991 - 8861801 6 chr1 9881162 9884464 - 9815625 7 chr1 9881162 9884464 - 9881150 8 chr1 9881162 9887404 - 9815625 9 chr1 9881162 9887404 - 9881150 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 3078934 1 chr1 3144471 3146364 - 3144459 2 chr1 5631745 5640565 + 5566208 3 chr1 5631745 5640565 + 5631733 4 chr1 8861813 8870991 - 8796276 5 chr1 8861813 8870991 - 8861801 6 chr1 9881162 9884464 - 9815625 7 chr1 9881162 9884464 - 9881150 8 chr1 9881162 9887404 - 9815625 9 chr1 9881162 9887404 - 9881150 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 3078934 1 chr1 3144471 3146364 - 3144459 2 chr1 5631745 5640565 + 5566208 3 chr1 5631745 5640565 + 5631733 4 chr1 8861813 8870991 - 8796276 5 chr1 8861813 8870991 - 8861801 6 chr1 9881162 9884464 - 9815625 7 chr1 9881162 9884464 - 9881150 8 chr1 9881162 9887404 - 9815625 9 chr1 9881162 9887404 - 9881150 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5opxkvy4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5opxkvy4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 + 2485382 3 chr1 5631745 5640565 + 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 - 1010172 9 chr1 9881162 9887404 - 4240598 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 5631745 | 5640565 | a | 0 | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | chr1 | 9881162 | 9884464 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 9881162 | 9887404 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | | chr1 | 8861813 | 8870991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 3144471 3146364 - 2485382 5 chr1 3144471 3146364 - 5715450 0 chr1 5631745 5640565 + 2485382 1 chr1 5631745 5640565 + 3221249 8 chr1 8861813 8870991 - 1010172 9 chr1 8861813 8870991 - 3221249 2 chr1 9881162 9884464 - 1010172 3 chr1 9881162 9884464 - 4240598 6 chr1 9881162 9887404 - 1010172 7 chr1 9881162 9887404 - 4240598 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 + 2485382 3 chr1 5631745 5640565 + 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 - 1010172 9 chr1 9881162 9887404 - 4240598 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 + 2485382 3 chr1 5631745 5640565 + 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 - 1010172 9 chr1 9881162 9887404 - 4240598 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3146364 - 2485382 1 chr1 3144471 3146364 - 5715450 2 chr1 5631745 5640565 + 2485382 3 chr1 5631745 5640565 + 3221249 4 chr1 8861813 8870991 - 1010172 5 chr1 8861813 8870991 - 3221249 6 chr1 9881162 9884464 - 1010172 7 chr1 9881162 9884464 - 4240598 8 chr1 9881162 9887404 - 1010172 9 chr1 9881162 9887404 - 4240598 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9c4xtuw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9c4xtuw4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 4 chr1 9881162 9881419 - 9880903 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5632002 | a | 0 | ... | | chr1 | 9881162 | 9881419 | a | 0 | ... | | chr1 | 3144471 | 3144728 | a | 0 | ... | | chr1 | 9881162 | 9881419 | a | 0 | ... | | chr1 | 8861813 | 8862070 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3144471 3144728 - 3144212 0 chr1 5631745 5632002 - 5631486 4 chr1 8861813 8862070 - 8861554 1 chr1 9881162 9881419 - 9880903 3 chr1 9881162 9881419 - 9880903 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 4 chr1 9881162 9881419 - 9880903 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 4 chr1 9881162 9881419 - 9880903 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 4 chr1 9881162 9881419 - 9880903 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuk_96f9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuk_96f9s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5632002 | a | 0 | ... | | chr1 | 3144471 | 3144728 | a | 0 | ... | | chr1 | 9881162 | 9881419 | a | 0 | ... | | chr1 | 8861813 | 8862070 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3144471 3144728 - 3144212 0 chr1 5631745 5632002 - 5631486 3 chr1 8861813 8862070 - 8861554 2 chr1 9881162 9881419 - 9880903 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsas9u5ve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsas9u5ve/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5631745 | 5632002 | a | 0 | ... | | chr1 | 3144471 | 3144728 | a | 0 | ... | | chr1 | 9881162 | 9881419 | a | 0 | ... | | chr1 | 8861813 | 8862070 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3144471 3144728 - 3144212 0 chr1 5631745 5632002 - 5631486 3 chr1 8861813 8862070 - 8861554 2 chr1 9881162 9881419 - 9880903 df2 Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Actual Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Expected Chromosome Start End Strand Distance 0 chr1 3144471 3144728 - 3144212 1 chr1 5631745 5632002 - 5631486 2 chr1 8861813 8862070 - 8861554 3 chr1 9881162 9881419 - 9880903 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzkhqfrjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzkhqfrjh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 2954 - 4194650 1 chr1 2 2954 - 8439305 2 chr1 698738 701690 + 3495914 3 chr1 698738 701690 + 7740569 4 chr1 2481278 2491278 - 1706326 5 chr1 2481278 2491278 - 5950981 6 chr1 7407375 7410327 - 1031932 7 chr1 7407375 7410327 - 3206855 8 chr1 9413409 9418115 - 967928 9 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 16 chrY 1913264 1913266 - 702332 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 698738 | 701690 | a | 0 | ... | | chr1 | 698738 | 701690 | a | 0 | ... | | chr1 | 2481278 | 2491278 | a | 0 | ... | | chr1 | 2481278 | 2491278 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7407375 | 7410327 | a | 0 | ... | | chr1 | 7407375 | 7410327 | a | 0 | ... | | chr1 | 9444205 | 9447157 | a | 0 | ... | | chr1 | 9444205 | 9447157 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 2954 - 4194650 5 chr1 2 2954 - 8439305 0 chr1 698738 701690 + 3495914 1 chr1 698738 701690 + 7740569 12 chrY 1913264 1913266 - 702332 2 chr1 2481278 2491278 - 1706326 3 chr1 2481278 2491278 - 5950981 8 chr1 7407375 7410327 - 1031932 9 chr1 7407375 7410327 - 3206855 6 chr1 9413409 9418115 - 967928 7 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 df2 Chromosome Start End Strand Distance 0 chr1 2 2954 - 4194650 1 chr1 2 2954 - 8439305 2 chr1 698738 701690 + 3495914 3 chr1 698738 701690 + 7740569 16 chrY 1913264 1913266 - 702332 4 chr1 2481278 2491278 - 1706326 5 chr1 2481278 2491278 - 5950981 6 chr1 7407375 7410327 - 1031932 7 chr1 7407375 7410327 - 3206855 8 chr1 9413409 9418115 - 967928 9 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 Actual Chromosome Start End Strand Distance 0 chr1 2 2954 - 4194650 1 chr1 2 2954 - 8439305 2 chr1 698738 701690 + 3495914 3 chr1 698738 701690 + 7740569 4 chr1 2481278 2491278 - 1706326 5 chr1 2481278 2491278 - 5950981 6 chr1 7407375 7410327 - 1031932 7 chr1 7407375 7410327 - 3206855 8 chr1 9413409 9418115 - 967928 9 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 12 chrY 1913264 1913266 - 702332 Expected Chromosome Start End Strand Distance 0 chr1 2 2954 - 4194650 1 chr1 2 2954 - 8439305 2 chr1 698738 701690 + 3495914 3 chr1 698738 701690 + 7740569 4 chr1 2481278 2491278 - 1706326 5 chr1 2481278 2491278 - 5950981 6 chr1 7407375 7410327 - 1031932 7 chr1 7407375 7410327 - 3206855 8 chr1 9413409 9418115 - 967928 9 chr1 9413409 9418115 - 5212889 10 chr1 9444205 9447157 - 998724 11 chr1 9444205 9447157 - 5243685 12 chrY 1913264 1913266 - 702332 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvwbp267i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwbp267i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 698738 701690 - 698481 2 chr1 2481278 2491278 - 2481021 3 chr1 7407375 7410327 + 7407118 4 chr1 9413409 9418115 + 9413152 5 chr1 9444205 9447157 - 9443948 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9413409 | 9418115 | a | 0 | ... | | chr1 | 7407375 | 7410327 | a | 0 | ... | | chr1 | 2481278 | 2491278 | a | 0 | ... | | chr1 | 698738 | 701690 | a | 0 | ... | | chr1 | 9444205 | 9447157 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 698738 701690 - 698481 2 chr1 2481278 2491278 - 2481021 1 chr1 7407375 7410327 + 7407118 0 chr1 9413409 9418115 + 9413152 4 chr1 9444205 9447157 - 9443948 df2 Chromosome Start End Strand Distance 1 chr1 698738 701690 - 698481 2 chr1 2481278 2491278 - 2481021 3 chr1 7407375 7410327 + 7407118 4 chr1 9413409 9418115 + 9413152 5 chr1 9444205 9447157 - 9443948 Actual Chromosome Start End Strand Distance 0 chr1 698738 701690 - 698481 1 chr1 2481278 2491278 - 2481021 2 chr1 7407375 7410327 + 7407118 3 chr1 9413409 9418115 + 9413152 4 chr1 9444205 9447157 - 9443948 Expected Chromosome Start End Strand Distance 0 chr1 698738 701690 - 698481 1 chr1 2481278 2491278 - 2481021 2 chr1 7407375 7410327 + 7407118 3 chr1 9413409 9418115 + 9413152 4 chr1 9444205 9447157 - 9443948 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwxzoxbkf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxzoxbkf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 2954 - 1910311 1 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 3 chr1 7407375 7410327 + 5493855 4 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9413409 | 9418115 | a | 0 | ... | | chr1 | 7407375 | 7410327 | a | 0 | ... | | chr1 | 2481278 | 2491278 | a | 0 | ... | | chr1 | 698738 | 701690 | a | 0 | ... | | chr1 | 2 | 2954 | a | 0 | ... | | chr1 | 9444205 | 9447157 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 2 2954 - 1910311 3 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 1 chr1 7407375 7410327 + 5493855 0 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 df2 Chromosome Start End Strand Distance 0 chr1 2 2954 - 1910311 1 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 3 chr1 7407375 7410327 + 5493855 4 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 Actual Chromosome Start End Strand Distance 0 chr1 2 2954 - 1910311 1 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 3 chr1 7407375 7410327 + 5493855 4 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 Expected Chromosome Start End Strand Distance 0 chr1 2 2954 - 1910311 1 chr1 698738 701690 - 1211575 2 chr1 2481278 2491278 - 567758 3 chr1 7407375 7410327 + 5493855 4 chr1 9413409 9418115 + 7499889 5 chr1 9444205 9447157 - 7530685 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3ys96l2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3ys96l2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 65537 65794 - 65278 5 chr1 65537 65794 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 df2 Chromosome Start End Strand Distance 4 chr1 65537 65794 - 65278 5 chr1 65537 65794 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxlfaz_i7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlfaz_i7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 65537 65794 - 65278 5 chr1 65537 65794 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 df2 Chromosome Start End Strand Distance 4 chr1 65537 65794 - 65278 5 chr1 65537 65794 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65278 1 chr1 65537 65794 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpupx3cmqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupx3cmqm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 261 - 65277 1 chr1 4 261 - 65277 2 chr1 4 5 - 65533 3 chr1 4 9 - 65529 4 chr1 65537 65794 - 65277 5 chr1 65537 65794 - 65531 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 4 | 261 | a | 0 | ... | | chr1 | 4 | 9 | a | 0 | ... | | chr1 | 4 | 261 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 4 5 - 65533 3 chr1 4 9 - 65529 2 chr1 4 261 - 65277 4 chr1 4 261 - 65277 0 chr1 65537 65794 - 65277 1 chr1 65537 65794 - 65531 df2 Chromosome Start End Strand Distance 2 chr1 4 5 - 65533 3 chr1 4 9 - 65529 0 chr1 4 261 - 65277 1 chr1 4 261 - 65277 4 chr1 65537 65794 - 65277 5 chr1 65537 65794 - 65531 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr1 4 261 - 65277 3 chr1 4 261 - 65277 4 chr1 65537 65794 - 65277 5 chr1 65537 65794 - 65531 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr1 4 261 - 65277 3 chr1 4 261 - 65277 4 chr1 65537 65794 - 65277 5 chr1 65537 65794 - 65531 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8sbnootx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8sbnootx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 261 - 65277 1 chr1 4 261 - 65277 2 chr1 4 5 - 65533 3 chr1 4 9 - 65529 6 chr2 4 261 - 65277 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 261 | a | 0 | ... | | chr1 | 4 | 9 | a | 0 | ... | | chr1 | 4 | 261 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr2 | 4 | 261 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 4 5 - 65533 1 chr1 4 9 - 65529 0 chr1 4 261 - 65277 2 chr1 4 261 - 65277 4 chr2 4 261 - 65277 df2 Chromosome Start End Strand Distance 2 chr1 4 5 - 65533 3 chr1 4 9 - 65529 0 chr1 4 261 - 65277 1 chr1 4 261 - 65277 6 chr2 4 261 - 65277 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr1 4 261 - 65277 3 chr1 4 261 - 65277 4 chr2 4 261 - 65277 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr1 4 261 - 65277 3 chr1 4 261 - 65277 4 chr2 4 261 - 65277 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp082usoju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp082usoju/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1345654 1352455 + 69202 1 chr1 1345654 1352455 + 93559 2 chr1 2356401 2365769 + 443297 3 chr1 2356401 2365769 + 928153 4 chr1 7085902 7095901 + 1533288 5 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2356401 | 2365769 | a | 0 | ... | | chr1 | 2356401 | 2365769 | a | 0 | ... | | chr1 | 7085902 | 7095901 | a | 0 | ... | | chr1 | 7085902 | 7095901 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8473657 | 8480066 | a | 0 | ... | | chr1 | 8473657 | 8480066 | a | 0 | ... | | chr1 | 10000000 | 10004190 | a | 0 | ... | | chr1 | 10000000 | 10004190 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1345654 1352455 + 69202 5 chr1 1345654 1352455 + 93559 0 chr1 2356401 2365769 + 443297 1 chr1 2356401 2365769 + 928153 2 chr1 7085902 7095901 + 1533288 3 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 df2 Chromosome Start End Strand Distance 0 chr1 1345654 1352455 + 69202 1 chr1 1345654 1352455 + 93559 2 chr1 2356401 2365769 + 443297 3 chr1 2356401 2365769 + 928153 4 chr1 7085902 7095901 + 1533288 5 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 Actual Chromosome Start End Strand Distance 0 chr1 1345654 1352455 + 69202 1 chr1 1345654 1352455 + 93559 2 chr1 2356401 2365769 + 443297 3 chr1 2356401 2365769 + 928153 4 chr1 7085902 7095901 + 1533288 5 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 Expected Chromosome Start End Strand Distance 0 chr1 1345654 1352455 + 69202 1 chr1 1345654 1352455 + 93559 2 chr1 2356401 2365769 + 443297 3 chr1 2356401 2365769 + 928153 4 chr1 7085902 7095901 + 1533288 5 chr1 7085902 7095901 + 2776430 6 chr1 7690326 7694655 - 934534 7 chr1 7690326 7694655 - 2177676 8 chr1 8473657 8480066 - 149123 9 chr1 8473657 8480066 - 1392265 10 chr1 10000000 10004190 - 123465 11 chr1 10000000 10004190 - 1367392 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1qdoiqzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qdoiqzf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1297 + 29071 1 chr1 1 1297 + 1247562 2 chr1 30367 33219 - 29071 3 chr1 30367 33219 - 1215640 4 chr1 1248858 1252096 + 169561 5 chr1 1248858 1252096 + 1215640 6 chr1 1421656 1428249 + 169561 7 chr1 1421656 1428249 + 1380817 8 chr1 2809065 2809560 + 1380817 9 chr1 2809065 2809560 + 1556970 10 chr1 8629188 8632609 + 1239722 11 chr1 8629188 8632609 + 5819629 12 chr1 9872330 9876536 + 1239722 13 chr1 9872330 9876536 + 7062771 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1421656 | 1428249 | a | 0 | ... | | chr1 | 1421656 | 1428249 | a | 0 | ... | | chr1 | 2809065 | 2809560 | a | 0 | ... | | chr1 | 2809065 | 2809560 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9872330 | 9876536 | a | 0 | ... | | chr1 | 9872330 | 9876536 | a | 0 | ... | | chr1 | 30367 | 33219 | a | 0 | ... | | chr1 | 30367 | 33219 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 1297 + 29071 5 chr1 1 1297 + 1247562 12 chr1 30367 33219 - 29071 13 chr1 30367 33219 - 1215640 8 chr1 1248858 1252096 + 169561 9 chr1 1248858 1252096 + 1215640 0 chr1 1421656 1428249 + 169561 1 chr1 1421656 1428249 + 1380817 2 chr1 2809065 2809560 + 1380817 3 chr1 2809065 2809560 + 1556970 6 chr1 8629188 8632609 + 1239722 7 chr1 8629188 8632609 + 5819629 10 chr1 9872330 9876536 + 1239722 11 chr1 9872330 9876536 + 7062771 df2 Chromosome Start End Strand Distance 0 chr1 1 1297 + 29071 1 chr1 1 1297 + 1247562 2 chr1 30367 33219 - 29071 3 chr1 30367 33219 - 1215640 4 chr1 1248858 1252096 + 169561 5 chr1 1248858 1252096 + 1215640 6 chr1 1421656 1428249 + 169561 7 chr1 1421656 1428249 + 1380817 8 chr1 2809065 2809560 + 1380817 9 chr1 2809065 2809560 + 1556970 10 chr1 8629188 8632609 + 1239722 11 chr1 8629188 8632609 + 5819629 12 chr1 9872330 9876536 + 1239722 13 chr1 9872330 9876536 + 7062771 Actual Chromosome Start End Strand Distance 0 chr1 1 1297 + 29071 1 chr1 1 1297 + 1247562 2 chr1 30367 33219 - 29071 3 chr1 30367 33219 - 1215640 4 chr1 1248858 1252096 + 169561 5 chr1 1248858 1252096 + 1215640 6 chr1 1421656 1428249 + 169561 7 chr1 1421656 1428249 + 1380817 8 chr1 2809065 2809560 + 1380817 9 chr1 2809065 2809560 + 1556970 10 chr1 8629188 8632609 + 1239722 11 chr1 8629188 8632609 + 5819629 12 chr1 9872330 9876536 + 1239722 13 chr1 9872330 9876536 + 7062771 Expected Chromosome Start End Strand Distance 0 chr1 1 1297 + 29071 1 chr1 1 1297 + 1247562 2 chr1 30367 33219 - 29071 3 chr1 30367 33219 - 1215640 4 chr1 1248858 1252096 + 169561 5 chr1 1248858 1252096 + 1215640 6 chr1 1421656 1428249 + 169561 7 chr1 1421656 1428249 + 1380817 8 chr1 2809065 2809560 + 1380817 9 chr1 2809065 2809560 + 1556970 10 chr1 8629188 8632609 + 1239722 11 chr1 8629188 8632609 + 5819629 12 chr1 9872330 9876536 + 1239722 13 chr1 9872330 9876536 + 7062771 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp19fsunr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19fsunr5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 941 - 2621516 1 chr1 2 942 - 2621515 2 chr1 30367 31307 - 30050 3 chr1 30367 31307 - 2591150 4 chr1 65537 66477 + 65220 5 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 8 chr1 2809065 2810005 + 186353 9 chr1 2809065 2810005 + 2808748 10 chr1 9872330 9872332 + 7249618 11 chr1 9872330 9872332 + 9872013 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 941 | a | 0 | ... | | chr1 | 30367 | 31307 | a | 0 | ... | | chr1 | 30367 | 31307 | a | 0 | ... | | chr1 | 2 | 942 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1 941 - 2621516 11 chr1 2 942 - 2621515 9 chr1 30367 31307 - 30050 10 chr1 30367 31307 - 2591150 2 chr1 65537 66477 + 65220 3 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 0 chr1 2809065 2810005 + 186353 1 chr1 2809065 2810005 + 2808748 4 chr1 9872330 9872332 + 7249618 5 chr1 9872330 9872332 + 9872013 df2 Chromosome Start End Strand Distance 0 chr1 1 941 - 2621516 1 chr1 2 942 - 2621515 2 chr1 30367 31307 - 30050 3 chr1 30367 31307 - 2591150 4 chr1 65537 66477 + 65220 5 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 8 chr1 2809065 2810005 + 186353 9 chr1 2809065 2810005 + 2808748 10 chr1 9872330 9872332 + 7249618 11 chr1 9872330 9872332 + 9872013 Actual Chromosome Start End Strand Distance 0 chr1 1 941 - 2621516 1 chr1 2 942 - 2621515 2 chr1 30367 31307 - 30050 3 chr1 30367 31307 - 2591150 4 chr1 65537 66477 + 65220 5 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 8 chr1 2809065 2810005 + 186353 9 chr1 2809065 2810005 + 2808748 10 chr1 9872330 9872332 + 7249618 11 chr1 9872330 9872332 + 9872013 Expected Chromosome Start End Strand Distance 0 chr1 1 941 - 2621516 1 chr1 2 942 - 2621515 2 chr1 30367 31307 - 30050 3 chr1 30367 31307 - 2591150 4 chr1 65537 66477 + 65220 5 chr1 65537 66477 + 2555980 6 chr1 1421656 1421658 - 1200799 7 chr1 1421656 1421658 - 1421339 8 chr1 2809065 2810005 + 186353 9 chr1 2809065 2810005 + 2808748 10 chr1 9872330 9872332 + 7249618 11 chr1 9872330 9872332 + 9872013 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpufjtvn24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufjtvn24/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | chr1 | 1421656 | 1421658 | a | 0 | ... | | chr1 | 30367 | 30368 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 4 chr1 65537 66477 - 65536 2 chr1 1421656 1421658 - 1421655 0 chr1 2809065 2810005 + 2809064 df2 Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 Actual Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Expected Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbk_mb4o_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbk_mb4o_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | chr1 | 1421656 | 1421658 | a | 0 | ... | | chr1 | 30367 | 30368 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 4 chr1 65537 66477 - 65536 2 chr1 1421656 1421658 - 1421655 0 chr1 2809065 2810005 + 2809064 df2 Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 Actual Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Expected Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdnoinqca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnoinqca/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2809065 | 2810005 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | | chr1 | 1421656 | 1421658 | a | 0 | ... | | chr1 | 30367 | 30368 | a | 0 | ... | | chr1 | 65537 | 66477 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 4 chr1 65537 66477 - 65536 2 chr1 1421656 1421658 - 1421655 0 chr1 2809065 2810005 + 2809064 df2 Chromosome Start End Strand Distance 1 chr1 30367 30368 - 30366 2 chr1 65537 66477 + 65536 3 chr1 65537 66477 - 65536 4 chr1 1421656 1421658 - 1421655 5 chr1 2809065 2810005 + 2809064 Actual Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Expected Chromosome Start End Strand Distance 0 chr1 30367 30368 - 30366 1 chr1 65537 66477 + 65536 2 chr1 65537 66477 - 65536 3 chr1 1421656 1421658 - 1421655 4 chr1 2809065 2810005 + 2809064 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyfm_wsiy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfm_wsiy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqj8ct8e4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqj8ct8e4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 2 chr1 1359680 1366401 - 978662 3 chr1 2649568 2652676 - 304506 4 chr1 5519069 5520984 - 3174007 5 chr1 7636786 7639758 + 5291724 6 chr1 7726109 7733000 + 5381047 7 chr1 8786725 8794271 + 6441663 8 chr1 9450560 9457184 + 7105498 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7726109 | 7733000 | a | 0 | ... | | chr1 | 660331 | 662849 | a | 0 | ... | | chr1 | 8786725 | 8794271 | a | 0 | ... | | chr1 | 9450560 | 9457184 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 3203 | a | 0 | ... | | chr1 | 1359680 | 1366401 | a | 0 | ... | | chr1 | 5519069 | 5520984 | a | 0 | ... | | chr1 | 2649568 | 2652676 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 6 chr1 1359680 1366401 - 978662 8 chr1 2649568 2652676 - 304506 7 chr1 5519069 5520984 - 3174007 4 chr1 7636786 7639758 + 5291724 0 chr1 7726109 7733000 + 5381047 2 chr1 8786725 8794271 + 6441663 3 chr1 9450560 9457184 + 7105498 df2 Chromosome Start End Strand Distance 0 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 2 chr1 1359680 1366401 - 978662 3 chr1 2649568 2652676 - 304506 4 chr1 5519069 5520984 - 3174007 5 chr1 7636786 7639758 + 5291724 6 chr1 7726109 7733000 + 5381047 7 chr1 8786725 8794271 + 6441663 8 chr1 9450560 9457184 + 7105498 Actual Chromosome Start End Strand Distance 0 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 2 chr1 1359680 1366401 - 978662 3 chr1 2649568 2652676 - 304506 4 chr1 5519069 5520984 - 3174007 5 chr1 7636786 7639758 + 5291724 6 chr1 7726109 7733000 + 5381047 7 chr1 8786725 8794271 + 6441663 8 chr1 9450560 9457184 + 7105498 Expected Chromosome Start End Strand Distance 0 chr1 1 3203 + 2341860 1 chr1 660331 662849 + 1682214 2 chr1 1359680 1366401 - 978662 3 chr1 2649568 2652676 - 304506 4 chr1 5519069 5520984 - 3174007 5 chr1 7636786 7639758 + 5291724 6 chr1 7726109 7733000 + 5381047 7 chr1 8786725 8794271 + 6441663 8 chr1 9450560 9457184 + 7105498 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcuyp1ruk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcuyp1ruk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8bzozm3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8bzozm3n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1o82jqot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o82jqot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj4feljz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4feljz6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf4lwhyn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4lwhyn8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp4aki9p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4aki9p4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp432yt1_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp432yt1_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpywjja3bd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpywjja3bd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjmao942r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjmao942r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 353014 + 277624 1 chr1 347873 353014 + 3257613 2 chr1 4453913 4463913 + 217294 3 chr1 4453913 4463913 + 836639 4 chr1 7382753 7384666 + 123943 5 chr1 7382753 7384666 + 2209390 6 chr1 8032598 8033237 + 773788 7 chr1 8032598 8033237 + 1560819 8 chr1 8696361 8697120 + 896936 9 chr1 8696361 8697120 + 1437551 14 chr22 7230165 7236079 - 100624 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8033237 | a | 0 | ... | | chr1 | 8032598 | 8033237 | a | 0 | ... | | chr1 | 8696361 | 8697120 | a | 0 | ... | | chr1 | 8696361 | 8697120 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7382753 | 7384666 | a | 0 | ... | | chr1 | 7382753 | 7384666 | a | 0 | ... | | chr1 | 4453913 | 4463913 | a | 0 | ... | | chr1 | 4453913 | 4463913 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 347873 353014 + 277624 5 chr1 347873 353014 + 3257613 8 chr1 4453913 4463913 + 217294 9 chr1 4453913 4463913 + 836639 10 chr22 7230165 7236079 - 100624 6 chr1 7382753 7384666 + 123943 7 chr1 7382753 7384666 + 2209390 0 chr1 8032598 8033237 + 773788 1 chr1 8032598 8033237 + 1560819 2 chr1 8696361 8697120 + 896936 3 chr1 8696361 8697120 + 1437551 df2 Chromosome Start End Strand Distance 0 chr1 347873 353014 + 277624 1 chr1 347873 353014 + 3257613 2 chr1 4453913 4463913 + 217294 3 chr1 4453913 4463913 + 836639 14 chr22 7230165 7236079 - 100624 4 chr1 7382753 7384666 + 123943 5 chr1 7382753 7384666 + 2209390 6 chr1 8032598 8033237 + 773788 7 chr1 8032598 8033237 + 1560819 8 chr1 8696361 8697120 + 896936 9 chr1 8696361 8697120 + 1437551 Actual Chromosome Start End Strand Distance 0 chr1 347873 353014 + 277624 1 chr1 347873 353014 + 3257613 2 chr1 4453913 4463913 + 217294 3 chr1 4453913 4463913 + 836639 4 chr1 7382753 7384666 + 123943 5 chr1 7382753 7384666 + 2209390 6 chr1 8032598 8033237 + 773788 7 chr1 8032598 8033237 + 1560819 8 chr1 8696361 8697120 + 896936 9 chr1 8696361 8697120 + 1437551 10 chr22 7230165 7236079 - 100624 Expected Chromosome Start End Strand Distance 0 chr1 347873 353014 + 277624 1 chr1 347873 353014 + 3257613 2 chr1 4453913 4463913 + 217294 3 chr1 4453913 4463913 + 836639 4 chr1 7382753 7384666 + 123943 5 chr1 7382753 7384666 + 2209390 6 chr1 8032598 8033237 + 773788 7 chr1 8032598 8033237 + 1560819 8 chr1 8696361 8697120 + 896936 9 chr1 8696361 8697120 + 1437551 10 chr22 7230165 7236079 - 100624 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzqw2n_g6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqw2n_g6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282335 4 chr1 4453913 4453920 - 4388375 3 chr1 7382753 7382998 - 7317215 0 chr1 8032598 8032599 - 7967060 1 chr1 8696361 8696362 - 8630823 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw1q4ob8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1q4ob8k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 8 chr2 2080758 2087840 - 2014965 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | | chr2 | 2080758 | 2087840 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282335 5 chr2 2080758 2087840 - 2014965 4 chr1 4453913 4453920 - 4388375 3 chr1 7382753 7382998 - 7317215 0 chr1 8032598 8032599 - 7967060 1 chr1 8696361 8696362 - 8630823 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 8 chr2 2080758 2087840 - 2014965 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplbcsbtgb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbcsbtgb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 8 chr2 2080758 2087840 - 2014965 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | | chr2 | 2080758 | 2087840 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282335 5 chr2 2080758 2087840 - 2014965 4 chr1 4453913 4453920 - 4388375 3 chr1 7382753 7382998 - 7317215 0 chr1 8032598 8032599 - 7967060 1 chr1 8696361 8696362 - 8630823 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 8 chr2 2080758 2087840 - 2014965 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp1q8n2fa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1q8n2fa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 7 chr2 2080758 2087840 - 2014965 8 chr2 6821396 6825749 - 6755603 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | | chr2 | 6821396 | 6825749 | a | 0 | ... | | chr2 | 2080758 | 2087840 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282335 6 chr2 2080758 2087840 - 2014965 4 chr1 4453913 4453920 - 4388375 5 chr2 6821396 6825749 - 6755603 3 chr1 7382753 7382998 - 7317215 0 chr1 8032598 8032599 - 7967060 1 chr1 8696361 8696362 - 8630823 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 7 chr2 2080758 2087840 - 2014965 1 chr1 4453913 4453920 - 4388375 8 chr2 6821396 6825749 - 6755603 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 6 chr2 6821396 6825749 - 6755603 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282335 1 chr1 4453913 4453920 - 4388375 2 chr1 7382753 7382998 - 7317215 3 chr1 8032598 8032599 - 7967060 4 chr1 8696361 8696362 - 8630823 5 chr2 2080758 2087840 - 2014965 6 chr2 6821396 6825749 - 6755603 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuktpqhp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuktpqhp6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282328 1 chr1 4453913 4453920 - 4388368 2 chr1 7382753 7382998 - 7317208 3 chr1 8032598 8032599 - 7967053 4 chr1 8696361 8696362 - 8630816 7 chr2 2080758 2087840 - 2080754 8 chr2 6821396 6825749 - 6821392 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8032598 | 8032599 | a | 0 | ... | | chr1 | 8696361 | 8696362 | a | 0 | ... | | chr1 | 347873 | 355298 | a | 0 | ... | | chr1 | 7382753 | 7382998 | a | 0 | ... | | chr1 | 4453913 | 4453920 | a | 0 | ... | | chr2 | 6821396 | 6825749 | a | 0 | ... | | chr2 | 2080758 | 2087840 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 347873 355298 - 282328 6 chr2 2080758 2087840 - 2080754 4 chr1 4453913 4453920 - 4388368 5 chr2 6821396 6825749 - 6821392 3 chr1 7382753 7382998 - 7317208 0 chr1 8032598 8032599 - 7967053 1 chr1 8696361 8696362 - 8630816 df2 Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282328 7 chr2 2080758 2087840 - 2080754 1 chr1 4453913 4453920 - 4388368 8 chr2 6821396 6825749 - 6821392 2 chr1 7382753 7382998 - 7317208 3 chr1 8032598 8032599 - 7967053 4 chr1 8696361 8696362 - 8630816 Actual Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282328 1 chr1 4453913 4453920 - 4388368 2 chr1 7382753 7382998 - 7317208 3 chr1 8032598 8032599 - 7967053 4 chr1 8696361 8696362 - 8630816 5 chr2 2080758 2087840 - 2080754 6 chr2 6821396 6825749 - 6821392 Expected Chromosome Start End Strand Distance 0 chr1 347873 355298 - 282328 1 chr1 4453913 4453920 - 4388368 2 chr1 7382753 7382998 - 7317208 3 chr1 8032598 8032599 - 7967053 4 chr1 8696361 8696362 - 8630816 5 chr2 2080758 2087840 - 2080754 6 chr2 6821396 6825749 - 6821392 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf_798kt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_798kt4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 1 chr1 9 1368 - 64170 2 chr1 9 8202 - 57336 3 chr1 65537 70914 - 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9 | 10 | a | 0 | ... | | chr1 | 65537 | 70914 | a | 0 | ... | | chr1 | 9 | 1368 | a | 0 | ... | | chr1 | 9 | 8202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 2 chr1 9 1368 - 64170 3 chr1 9 8202 - 57336 1 chr1 65537 70914 - 65280 df2 Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 1 chr1 9 1368 - 64170 2 chr1 9 8202 - 57336 3 chr1 65537 70914 - 65280 Actual Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 1 chr1 9 1368 - 64170 2 chr1 9 8202 - 57336 3 chr1 65537 70914 - 65280 Expected Chromosome Start End Strand Distance 0 chr1 9 10 + 65528 1 chr1 9 1368 - 64170 2 chr1 9 8202 - 57336 3 chr1 65537 70914 - 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq_vgsdck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq_vgsdck/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 858392 861950 - 851397 3 chr1 858392 861950 - 2919506 0 chr1 7364263 7372460 + 1955678 1 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0szlemom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0szlemom/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 858392 861950 - 851397 3 chr1 858392 861950 - 2919506 0 chr1 7364263 7372460 + 1955678 1 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 851397 1 chr1 858392 861950 - 2919506 2 chr1 7364263 7372460 + 1955678 3 chr1 7364263 7372460 + 2643191 4 chr1 7364263 7373652 - 1955678 5 chr1 7364263 7373652 - 2643191 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo3humml5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo3humml5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 792855 1 chr1 858392 861950 - 858383 2 chr1 7364263 7372460 + 7298726 3 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 858392 861950 - 792855 3 chr1 858392 861950 - 858383 0 chr1 7364263 7372460 + 7298726 1 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 792855 1 chr1 858392 861950 - 858383 2 chr1 7364263 7372460 + 7298726 3 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 792855 1 chr1 858392 861950 - 858383 2 chr1 7364263 7372460 + 7298726 3 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 792855 1 chr1 858392 861950 - 858383 2 chr1 7364263 7372460 + 7298726 3 chr1 7364263 7372460 + 7364254 4 chr1 7364263 7373652 - 7298726 5 chr1 7364263 7373652 - 7364254 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgqq87cey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqq87cey/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 6502314 1 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7364263 | 7372460 | a | 0 | ... | | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 858392 861950 - 6502314 0 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 6502314 1 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 6502314 1 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 6502314 1 chr1 7364263 7372460 + 6502314 2 chr1 7364263 7373652 - 6502314 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi37zx17t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi37zx17t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 1 chr1 7364263 7372460 - 7363947 2 chr1 7364263 7373652 - 7363947 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 858392 | 861950 | a | 0 | ... | | chr1 | 7364263 | 7373652 | a | 0 | ... | | chr1 | 7364263 | 7372460 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 2 chr1 7364263 7372460 - 7363947 1 chr1 7364263 7373652 - 7363947 df2 Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 1 chr1 7364263 7372460 - 7363947 2 chr1 7364263 7373652 - 7363947 Actual Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 1 chr1 7364263 7372460 - 7363947 2 chr1 7364263 7373652 - 7363947 Expected Chromosome Start End Strand Distance 0 chr1 858392 861950 - 858076 1 chr1 7364263 7372460 - 7363947 2 chr1 7364263 7373652 - 7363947 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplait83vw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplait83vw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr10 9925858 9926922 - 9925542 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr10 | 9925858 | 9926922 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9925542 df2 Chromosome Start End Strand Distance 3 chr10 9925858 9926922 - 9925542 Actual Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9925542 Expected Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9925542 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpabskdmn6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabskdmn6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr10 9925858 9926922 - 9919794 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr10 | 9925858 | 9926922 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9919794 df2 Chromosome Start End Strand Distance 3 chr10 9925858 9926922 - 9919794 Actual Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9919794 Expected Chromosome Start End Strand Distance 0 chr10 9925858 9926922 - 9919794 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5w6vitwe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5w6vitwe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1156855 1162997 - 1099643 9 chr1 1156855 1162997 - 1716765 6 chr1 3548283 3548906 + 663688 7 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 0 chr1 6767787 6777786 + 1367537 1 chr1 6767787 6777786 + 2111800 2 chr1 6886548 6887717 + 1257606 3 chr1 6886548 6887717 + 2001869 df2 Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Actual Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Expected Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvrrfy5wz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrrfy5wz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1156855 1162997 - 1099643 9 chr1 1156855 1162997 - 1716765 6 chr1 3548283 3548906 + 663688 7 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 0 chr1 6767787 6777786 + 1367537 1 chr1 6767787 6777786 + 2111800 2 chr1 6886548 6887717 + 1257606 3 chr1 6886548 6887717 + 2001869 df2 Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Actual Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Expected Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1099643 1 chr1 1156855 1162997 - 1716765 2 chr1 3548283 3548906 + 663688 3 chr1 3548283 3548906 + 3491071 4 chr1 5862024 5864160 + 2281163 5 chr1 5862024 5864160 + 2977429 6 chr1 6767787 6777786 + 1367537 7 chr1 6767787 6777786 + 2111800 8 chr1 6886548 6887717 + 1257606 9 chr1 6886548 6887717 + 2001869 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpboqdlqmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpboqdlqmr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1091062 1 chr1 1156855 1162997 - 1156595 2 chr1 3548283 3548906 + 3482490 3 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 6 chr1 6767787 6777786 + 6701994 7 chr1 6767787 6777786 + 6767527 8 chr1 6886548 6887717 + 6820755 9 chr1 6886548 6887717 + 6886288 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6767787 | 6777786 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | chr1 | 6886548 | 6887717 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 3548283 | 3548906 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | | chr1 | 1156855 | 1162997 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1156855 1162997 - 1091062 9 chr1 1156855 1162997 - 1156595 6 chr1 3548283 3548906 + 3482490 7 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 0 chr1 6767787 6777786 + 6701994 1 chr1 6767787 6777786 + 6767527 2 chr1 6886548 6887717 + 6820755 3 chr1 6886548 6887717 + 6886288 df2 Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1091062 1 chr1 1156855 1162997 - 1156595 2 chr1 3548283 3548906 + 3482490 3 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 6 chr1 6767787 6777786 + 6701994 7 chr1 6767787 6777786 + 6767527 8 chr1 6886548 6887717 + 6820755 9 chr1 6886548 6887717 + 6886288 Actual Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1091062 1 chr1 1156855 1162997 - 1156595 2 chr1 3548283 3548906 + 3482490 3 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 6 chr1 6767787 6777786 + 6701994 7 chr1 6767787 6777786 + 6767527 8 chr1 6886548 6887717 + 6820755 9 chr1 6886548 6887717 + 6886288 Expected Chromosome Start End Strand Distance 0 chr1 1156855 1162997 - 1091062 1 chr1 1156855 1162997 - 1156595 2 chr1 3548283 3548906 + 3482490 3 chr1 3548283 3548906 + 3548023 4 chr1 5862024 5864160 + 5796231 5 chr1 5862024 5864160 + 5861764 6 chr1 6767787 6777786 + 6701994 7 chr1 6767787 6777786 + 6767527 8 chr1 6886548 6887717 + 6820755 9 chr1 6886548 6887717 + 6886288 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpue7crmba/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpue7crmba/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 3 chr2 4 6 - 74 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 9 | a | 0 | ... | | chr2 | 4 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 2 chr2 4 6 - 74 1 chr1 4 9 - 65529 df2 Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 3 chr2 4 6 - 74 1 chr1 4 9 - 65529 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 6 - 74 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 6 - 74 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpofdqf06w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofdqf06w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 5 - 75 3 chr2 4 6 - 74 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 9 | a | 0 | ... | | chr2 | 4 | 5 | a | 0 | ... | | chr2 | 4 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr2 4 5 - 75 0 chr1 4 5 - 65533 3 chr2 4 6 - 74 1 chr1 4 9 - 65529 df2 Chromosome Start End Strand Distance 2 chr2 4 5 - 75 0 chr1 4 5 - 65533 3 chr2 4 6 - 74 1 chr1 4 9 - 65529 Actual Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 5 - 75 3 chr2 4 6 - 74 Expected Chromosome Start End Strand Distance 0 chr1 4 5 - 65533 1 chr1 4 9 - 65529 2 chr2 4 5 - 75 3 chr2 4 6 - 74 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48siqggx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48siqggx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5mgfr8kx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mgfr8kx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjclx042r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjclx042r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5918092 5918311 - 21998 1 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 4 chr1 8966121 8966122 - 3070027 5 chr1 8966121 8966122 - 3093082 6 chr1 9519744 9526725 + 3623650 7 chr1 9519744 9526725 + 3646705 9 chr14 4273233 4280094 + 976476 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9519744 | 9526725 | a | 0 | ... | | chr1 | 9519744 | 9526725 | a | 0 | ... | | chr1 | 8340730 | 8343567 | a | 0 | ... | | chr1 | 8340730 | 8343567 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5918092 | 5918311 | a | 0 | ... | | chr1 | 5918092 | 5918311 | a | 0 | ... | | chr1 | 8966121 | 8966122 | a | 0 | ... | | chr1 | 8966121 | 8966122 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr14 4273233 4280094 + 976476 4 chr1 5918092 5918311 - 21998 5 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 6 chr1 8966121 8966122 - 3070027 7 chr1 8966121 8966122 - 3093082 0 chr1 9519744 9526725 + 3623650 1 chr1 9519744 9526725 + 3646705 df2 Chromosome Start End Strand Distance 9 chr14 4273233 4280094 + 976476 0 chr1 5918092 5918311 - 21998 1 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 4 chr1 8966121 8966122 - 3070027 5 chr1 8966121 8966122 - 3093082 6 chr1 9519744 9526725 + 3623650 7 chr1 9519744 9526725 + 3646705 Actual Chromosome Start End Strand Distance 0 chr1 5918092 5918311 - 21998 1 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 4 chr1 8966121 8966122 - 3070027 5 chr1 8966121 8966122 - 3093082 6 chr1 9519744 9526725 + 3623650 7 chr1 9519744 9526725 + 3646705 8 chr14 4273233 4280094 + 976476 Expected Chromosome Start End Strand Distance 0 chr1 5918092 5918311 - 21998 1 chr1 5918092 5918311 - 45053 2 chr1 8340730 8343567 + 2444636 3 chr1 8340730 8343567 + 2467691 4 chr1 8966121 8966122 - 3070027 5 chr1 8966121 8966122 - 3093082 6 chr1 9519744 9526725 + 3623650 7 chr1 9519744 9526725 + 3646705 8 chr14 4273233 4280094 + 976476 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx18qc56g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx18qc56g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4420 | a | 0 | ... | | chr12 | 6 | 263 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 df2 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Expected Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2pz6i6j_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2pz6i6j_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4420 | a | 0 | ... | | chr12 | 6 | 263 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 df2 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Expected Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8po1tmtn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8po1tmtn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4420 | a | 0 | ... | | chr12 | 6 | 263 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 df2 Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Expected Chromosome Start End Strand Distance 0 chr1 1 4420 - 2442 1 chr12 6 263 - 6599 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj4y65njs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4y65njs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg_1ffd_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_1ffd_z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 258 + 65280 2 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 65536 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 258 + 65280 2 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 258 + 65280 2 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 258 + 65280 2 chr1 1 258 - 65280 3 chr1 1 258 - 65280 4 chr1 1 258 - 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsrh6qa5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsrh6qa5l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 6 chr8 680946 685979 + 658932 7 chrM 10000000 10003046 + 9477394 8 chrM 10000000 10009242 - 9477394 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10010000 | a | 0 | ... | | chr1 | 10000000 | 10010000 | a | 0 | ... | | chr8 | 680946 | 685979 | a | 0 | ... | | chrM | 10000000 | 10003046 | a | 0 | ... | | chrM | 10000000 | 10009242 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr8 680946 685979 + 658932 3 chrM 10000000 10003046 + 9477394 4 chrM 10000000 10009242 - 9477394 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 df2 Chromosome Start End Strand Distance 6 chr8 680946 685979 + 658932 7 chrM 10000000 10003046 + 9477394 8 chrM 10000000 10009242 - 9477394 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 Actual Chromosome Start End Strand Distance 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 2 chr8 680946 685979 + 658932 3 chrM 10000000 10003046 + 9477394 4 chrM 10000000 10009242 - 9477394 Expected Chromosome Start End Strand Distance 0 chr1 10000000 10010000 + 46069 1 chr1 10000000 10010000 + 662016 2 chr8 680946 685979 + 658932 3 chrM 10000000 10003046 + 9477394 4 chrM 10000000 10009242 - 9477394 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe9ijo35d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9ijo35d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpma2n9aqq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma2n9aqq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr18 6284987 6287624 + 6284978 3 chr2 10000000 10002433 - 9997564 4 chr2 10000000 10002433 - 9999979 5 chr7 10000000 10000712 - 9999915 7 chrM 10000000 10003046 + 9997562 8 chrM 10000000 10009242 - 9997562 9 chrY 3329340 3336894 + 3329211 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 10000000 | 10002433 | a | 0 | ... | | chr2 | 10000000 | 10002433 | a | 0 | ... | | chr7 | 10000000 | 10000712 | a | 0 | ... | | chr18 | 6284987 | 6287624 | a | 0 | ... | | chrM | 10000000 | 10003046 | a | 0 | ... | | chrM | 10000000 | 10009242 | a | 0 | ... | | chrY | 3329340 | 3336894 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chrY 3329340 3336894 + 3329211 3 chr18 6284987 6287624 + 6284978 2 chr7 10000000 10000712 - 9999915 0 chr2 10000000 10002433 - 9997564 1 chr2 10000000 10002433 - 9999979 4 chrM 10000000 10003046 + 9997562 5 chrM 10000000 10009242 - 9997562 df2 Chromosome Start End Strand Distance 9 chrY 3329340 3336894 + 3329211 2 chr18 6284987 6287624 + 6284978 5 chr7 10000000 10000712 - 9999915 3 chr2 10000000 10002433 - 9997564 4 chr2 10000000 10002433 - 9999979 7 chrM 10000000 10003046 + 9997562 8 chrM 10000000 10009242 - 9997562 Actual Chromosome Start End Strand Distance 0 chr18 6284987 6287624 + 6284978 1 chr2 10000000 10002433 - 9997564 2 chr2 10000000 10002433 - 9999979 3 chr7 10000000 10000712 - 9999915 4 chrM 10000000 10003046 + 9997562 5 chrM 10000000 10009242 - 9997562 6 chrY 3329340 3336894 + 3329211 Expected Chromosome Start End Strand Distance 0 chr18 6284987 6287624 + 6284978 1 chr2 10000000 10002433 - 9997564 2 chr2 10000000 10002433 - 9999979 3 chr7 10000000 10000712 - 9999915 4 chrM 10000000 10003046 + 9997562 5 chrM 10000000 10009242 - 9997562 6 chrY 3329340 3336894 + 3329211 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5js1sztf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5js1sztf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 4 | 2437 | a | 0 | ... | | chr2 | 6 | 13 | a | 0 | ... | | chr2 | 7 | 12 | a | 0 | ... | | chr2 | 15 | 22 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 df2 Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 Actual Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Expected Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5pp6jl9v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pp6jl9v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 4 | 2437 | a | 0 | ... | | chr2 | 6 | 13 | a | 0 | ... | | chr2 | 7 | 12 | a | 0 | ... | | chr2 | 15 | 22 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 df2 Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 Actual Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Expected Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp22c0yq9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp22c0yq9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 4 | 2437 | a | 0 | ... | | chr2 | 6 | 13 | a | 0 | ... | | chr2 | 7 | 12 | a | 0 | ... | | chr2 | 15 | 22 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 df2 Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 Actual Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Expected Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_s3zbdsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_s3zbdsu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 4 | 2437 | a | 0 | ... | | chr2 | 6 | 13 | a | 0 | ... | | chr2 | 7 | 12 | a | 0 | ... | | chr2 | 15 | 22 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 df2 Chromosome Start End Strand Distance 1 chr2 4 2437 - 63101 2 chr2 6 13 - 65525 3 chr2 7 12 - 65526 4 chr2 15 22 - 65516 Actual Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Expected Chromosome Start End Strand Distance 0 chr2 4 2437 - 63101 1 chr2 6 13 - 65525 2 chr2 7 12 - 65526 3 chr2 15 22 - 65516 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt2rnz_jg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2rnz_jg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpskpa4m6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskpa4m6e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiwh8g_jm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiwh8g_jm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6eo033n0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6eo033n0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr12 | 9167475 | 9171432 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 df2 Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 Actual Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 Expected Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9092077 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmgr9ij2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmgr9ij2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr12 | 9167475 | 9171432 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 df2 Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 Actual Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 Expected Chromosome Start End Strand Distance 0 chr12 9167475 9171432 + 9101933 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl0rdtcws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0rdtcws/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr12 | 11 | 3968 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 df2 Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Actual Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Expected Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxzxycjv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxzxycjv6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr12 | 11 | 3968 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 df2 Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Actual Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Expected Chromosome Start End Strand Distance 0 chr12 11 3968 + 61570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphk503crf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphk503crf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 3650420 | 3652943 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 4 chr1 2841009 2849202 - 1333010 3 chr1 3650420 3652943 - 529269 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5hj7uv2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hj7uv2t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 3650420 | 3652943 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 4 chr1 2841009 2849202 - 1333010 3 chr1 3650420 3652943 - 529269 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3650420 3652943 - 529269 3 chr1 3753195 3761626 - 420586 4 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9eo5e3og/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9eo5e3og/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 3 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpodfnopen/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodfnopen/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 3 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzmk6l5_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmk6l5_9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2426061 | 2434994 | a | 0 | ... | | chr1 | 5646943 | 5650912 | a | 0 | ... | | chr1 | 3753195 | 3761626 | a | 0 | ... | | chr1 | 2841009 | 2849202 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 3 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 1 chr1 5646943 5650912 + 1456712 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2434994 + 1747218 1 chr1 2841009 2849202 - 1333010 2 chr1 3753195 3761626 - 420586 3 chr1 5646943 5650912 + 1456712 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps0l4fcrt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0l4fcrt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2426061 2426064 - 2425804 1 chr1 2841009 2841012 - 2840752 2 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3753195 | 3761216 | a | 0 | ... | | chr1 | 2426061 | 2426064 | a | 0 | ... | | chr1 | 2841009 | 2841012 | a | 0 | ... | | chr1 | 5646943 | 5646946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2426061 2426064 - 2425804 2 chr1 2841009 2841012 - 2840752 0 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 df2 Chromosome Start End Strand Distance 0 chr1 2426061 2426064 - 2425804 1 chr1 2841009 2841012 - 2840752 2 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 Actual Chromosome Start End Strand Distance 0 chr1 2426061 2426064 - 2425804 1 chr1 2841009 2841012 - 2840752 2 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 Expected Chromosome Start End Strand Distance 0 chr1 2426061 2426064 - 2425804 1 chr1 2841009 2841012 - 2840752 2 chr1 3753195 3761216 - 3752938 3 chr1 5646943 5646946 - 5646686 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmuy8xcyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmuy8xcyl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 6016 | a | 0 | ... | | chr1 | 2 | 6016 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 4 chr1 2071439 2074140 - 432071 5 chr1 2071439 2074140 - 708902 2 chr1 6824194 6832392 + 237914 3 chr1 6824194 6832392 + 2363578 8 chr1 6824194 6832946 - 237360 9 chr1 6824194 6832946 - 2363578 6 chr1 8134000 8141150 - 1055989 7 chr1 8134000 8141150 - 3673384 df2 Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Actual Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Expected Chromosome Start End Strand Distance 0 chr1 2 6016 + 123148 1 chr1 2 6016 + 1631545 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaktfu6i5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaktfu6i5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9003 | a | 0 | ... | | chr1 | 2 | 9003 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 4 chr1 2071439 2074140 - 432071 5 chr1 2071439 2074140 - 708902 2 chr1 6824194 6832392 + 237914 3 chr1 6824194 6832392 + 2363578 8 chr1 6824194 6832946 - 237360 9 chr1 6824194 6832946 - 2363578 6 chr1 8134000 8141150 - 1055989 7 chr1 8134000 8141150 - 3673384 df2 Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Actual Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Expected Chromosome Start End Strand Distance 0 chr1 2 9003 + 120161 1 chr1 2 9003 + 1628558 2 chr1 2071439 2074140 - 432071 3 chr1 2071439 2074140 - 708902 4 chr1 6824194 6832392 + 237914 5 chr1 6824194 6832392 + 2363578 6 chr1 6824194 6832946 - 237360 7 chr1 6824194 6832946 - 2363578 8 chr1 8134000 8141150 - 1055989 9 chr1 8134000 8141150 - 3673384 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuehurhwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuehurhwm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 1 chr1 2071439 2074140 - 2005900 2 chr1 2071439 2074140 - 2071174 3 chr1 6824194 6832392 + 6758655 4 chr1 6824194 6832392 + 6823929 5 chr1 6824194 6832946 - 6758655 6 chr1 6824194 6832946 - 6823929 7 chr1 8134000 8141150 - 8068461 8 chr1 8134000 8141150 - 8133735 10 chr2 6824194 6826141 - 6758655 11 chr2 6824194 6826141 - 6824193 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9003 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 2071439 | 2074140 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 3 chr1 2071439 2074140 - 2005900 4 chr1 2071439 2074140 - 2071174 9 chr2 6824194 6826141 - 6758655 10 chr2 6824194 6826141 - 6824193 1 chr1 6824194 6832392 + 6758655 2 chr1 6824194 6832392 + 6823929 7 chr1 6824194 6832946 - 6758655 8 chr1 6824194 6832946 - 6823929 5 chr1 8134000 8141150 - 8068461 6 chr1 8134000 8141150 - 8133735 df2 Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 1 chr1 2071439 2074140 - 2005900 2 chr1 2071439 2074140 - 2071174 10 chr2 6824194 6826141 - 6758655 11 chr2 6824194 6826141 - 6824193 3 chr1 6824194 6832392 + 6758655 4 chr1 6824194 6832392 + 6823929 5 chr1 6824194 6832946 - 6758655 6 chr1 6824194 6832946 - 6823929 7 chr1 8134000 8141150 - 8068461 8 chr1 8134000 8141150 - 8133735 Actual Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 1 chr1 2071439 2074140 - 2005900 2 chr1 2071439 2074140 - 2071174 3 chr1 6824194 6832392 + 6758655 4 chr1 6824194 6832392 + 6823929 5 chr1 6824194 6832946 - 6758655 6 chr1 6824194 6832946 - 6823929 7 chr1 8134000 8141150 - 8068461 8 chr1 8134000 8141150 - 8133735 9 chr2 6824194 6826141 - 6758655 10 chr2 6824194 6826141 - 6824193 Expected Chromosome Start End Strand Distance 0 chr1 2 9003 + 56535 1 chr1 2071439 2074140 - 2005900 2 chr1 2071439 2074140 - 2071174 3 chr1 6824194 6832392 + 6758655 4 chr1 6824194 6832392 + 6823929 5 chr1 6824194 6832946 - 6758655 6 chr1 6824194 6832946 - 6823929 7 chr1 8134000 8141150 - 8068461 8 chr1 8134000 8141150 - 8133735 9 chr2 6824194 6826141 - 6758655 10 chr2 6824194 6826141 - 6824193 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpud0qt429/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpud0qt429/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 1 chr1 2071439 2074140 - 2071432 2 chr1 2071439 2074140 - 2071436 3 chr1 6824194 6832392 + 6824187 4 chr1 6824194 6832392 + 6824191 5 chr1 6824194 6832946 - 6824187 6 chr1 6824194 6832946 - 6824191 7 chr1 8134000 8141150 - 8133993 8 chr1 8134000 8141150 - 8133997 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9003 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 6824194 | 6832392 | a | 0 | ... | | chr1 | 2071439 | 2074140 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 8134000 | 8141150 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | | chr1 | 6824194 | 6832946 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 3 chr1 2071439 2074140 - 2071432 4 chr1 2071439 2074140 - 2071436 1 chr1 6824194 6832392 + 6824187 2 chr1 6824194 6832392 + 6824191 7 chr1 6824194 6832946 - 6824187 8 chr1 6824194 6832946 - 6824191 5 chr1 8134000 8141150 - 8133993 6 chr1 8134000 8141150 - 8133997 df2 Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 1 chr1 2071439 2074140 - 2071432 2 chr1 2071439 2074140 - 2071436 3 chr1 6824194 6832392 + 6824187 4 chr1 6824194 6832392 + 6824191 5 chr1 6824194 6832946 - 6824187 6 chr1 6824194 6832946 - 6824191 7 chr1 8134000 8141150 - 8133993 8 chr1 8134000 8141150 - 8133997 Actual Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 1 chr1 2071439 2074140 - 2071432 2 chr1 2071439 2074140 - 2071436 3 chr1 6824194 6832392 + 6824187 4 chr1 6824194 6832392 + 6824191 5 chr1 6824194 6832946 - 6824187 6 chr1 6824194 6832946 - 6824191 7 chr1 8134000 8141150 - 8133993 8 chr1 8134000 8141150 - 8133997 Expected Chromosome Start End Strand Distance 0 chr1 2 9003 + 1 1 chr1 2071439 2074140 - 2071432 2 chr1 2071439 2074140 - 2071436 3 chr1 6824194 6832392 + 6824187 4 chr1 6824194 6832392 + 6824191 5 chr1 6824194 6832946 - 6824187 6 chr1 6824194 6832946 - 6824191 7 chr1 8134000 8141150 - 8133993 8 chr1 8134000 8141150 - 8133997 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpudk0uz62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudk0uz62/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 8 chr1 3 4 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 0 chr1 3 4 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 8 chr1 3 4 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 3 4 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 3 4 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqscl3i6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqscl3i6e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqnnd552/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqnnd552/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 8 chr1 3 4 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 0 chr1 3 4 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 8 chr1 3 4 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 3 4 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 2 1 chr1 1 2 - 2 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 3 4 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpse1zy4xs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpse1zy4xs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2393623 2399974 - 310353 1 chr1 2393623 2399974 - 356532 2 chr1 6863831 6865563 + 1660709 3 chr1 6863831 6865563 + 4098447 4 chr14 1132263 1132264 - 4765783 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6863831 | 6865563 | a | 0 | ... | | chr1 | 6863831 | 6865563 | a | 0 | ... | | chr1 | 2393623 | 2399974 | a | 0 | ... | | chr1 | 2393623 | 2399974 | a | 0 | ... | | chr14 | 1132263 | 1132264 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr14 1132263 1132264 - 4765783 2 chr1 2393623 2399974 - 310353 3 chr1 2393623 2399974 - 356532 0 chr1 6863831 6865563 + 1660709 1 chr1 6863831 6865563 + 4098447 df2 Chromosome Start End Strand Distance 4 chr14 1132263 1132264 - 4765783 0 chr1 2393623 2399974 - 310353 1 chr1 2393623 2399974 - 356532 2 chr1 6863831 6865563 + 1660709 3 chr1 6863831 6865563 + 4098447 Actual Chromosome Start End Strand Distance 0 chr1 2393623 2399974 - 310353 1 chr1 2393623 2399974 - 356532 2 chr1 6863831 6865563 + 1660709 3 chr1 6863831 6865563 + 4098447 4 chr14 1132263 1132264 - 4765783 Expected Chromosome Start End Strand Distance 0 chr1 2393623 2399974 - 310353 1 chr1 2393623 2399974 - 356532 2 chr1 6863831 6865563 + 1660709 3 chr1 6863831 6865563 + 4098447 4 chr14 1132263 1132264 - 4765783 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmr8kobvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmr8kobvi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 5814626 2 chr1 2756505 2765385 - 44860 3 chr1 2756505 2765385 - 5760887 4 chr1 8526271 8532264 - 5760887 5 chr1 8526271 8532264 - 5814626 9 chr7 1003501 1007391 + 7602428 10 chr7 1003501 1007391 + 7945813 11 chr7 8609818 8618678 - 334526 12 chr7 8609818 8618678 - 7602428 13 chr7 8953203 8953482 - 334526 14 chr7 8953203 8953482 - 7945813 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr7 | 8609818 | 8618678 | a | 0 | ... | | chr7 | 8609818 | 8618678 | a | 0 | ... | | chr7 | 8953203 | 8953482 | a | 0 | ... | | chr7 | 8953203 | 8953482 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr7 1003501 1007391 + 7602428 7 chr7 1003501 1007391 + 7945813 4 chr1 2710326 2711646 - 44860 5 chr1 2710326 2711646 - 5814626 0 chr1 2756505 2765385 - 44860 1 chr1 2756505 2765385 - 5760887 2 chr1 8526271 8532264 - 5760887 3 chr1 8526271 8532264 - 5814626 8 chr7 8609818 8618678 - 334526 9 chr7 8609818 8618678 - 7602428 10 chr7 8953203 8953482 - 334526 11 chr7 8953203 8953482 - 7945813 df2 Chromosome Start End Strand Distance 9 chr7 1003501 1007391 + 7602428 10 chr7 1003501 1007391 + 7945813 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 5814626 2 chr1 2756505 2765385 - 44860 3 chr1 2756505 2765385 - 5760887 4 chr1 8526271 8532264 - 5760887 5 chr1 8526271 8532264 - 5814626 11 chr7 8609818 8618678 - 334526 12 chr7 8609818 8618678 - 7602428 13 chr7 8953203 8953482 - 334526 14 chr7 8953203 8953482 - 7945813 Actual Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 5814626 2 chr1 2756505 2765385 - 44860 3 chr1 2756505 2765385 - 5760887 4 chr1 8526271 8532264 - 5760887 5 chr1 8526271 8532264 - 5814626 6 chr7 1003501 1007391 + 7602428 7 chr7 1003501 1007391 + 7945813 8 chr7 8609818 8618678 - 334526 9 chr7 8609818 8618678 - 7602428 10 chr7 8953203 8953482 - 334526 11 chr7 8953203 8953482 - 7945813 Expected Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 5814626 2 chr1 2756505 2765385 - 44860 3 chr1 2756505 2765385 - 5760887 4 chr1 8526271 8532264 - 5760887 5 chr1 8526271 8532264 - 5814626 6 chr7 1003501 1007391 + 7602428 7 chr7 1003501 1007391 + 7945813 8 chr7 8609818 8618678 - 334526 9 chr7 8609818 8618678 - 7602428 10 chr7 8953203 8953482 - 334526 11 chr7 8953203 8953482 - 7945813 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9w8_7ak1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9w8_7ak1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5767561 7 chr14 5898046 5902152 - 3141533 8 chr2 9027365 9030522 - 6268365 9 chr2 9027365 9030522 - 9027309 13 chrM 1881625 1883952 - 872554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chr14 | 5898046 | 5902152 | a | 0 | ... | | chrM | 1881625 | 1883952 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 9 chrM 1881625 1883952 - 872554 4 chr1 2710326 2711646 - 44860 5 chr1 2710326 2711646 - 2642143 0 chr1 2756505 2765385 - 2688322 1 chr1 2756505 2765385 - 2690968 8 chr14 5898046 5902152 - 3141533 2 chr1 8526271 8532264 - 5763798 3 chr1 8526271 8532264 - 5767561 6 chr2 9027365 9030522 - 6268365 7 chr2 9027365 9030522 - 9027309 df2 Chromosome Start End Strand Distance 13 chrM 1881625 1883952 - 872554 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 7 chr14 5898046 5902152 - 3141533 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5767561 8 chr2 9027365 9030522 - 6268365 9 chr2 9027365 9030522 - 9027309 Actual Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5767561 6 chr14 5898046 5902152 - 3141533 7 chr2 9027365 9030522 - 6268365 8 chr2 9027365 9030522 - 9027309 9 chrM 1881625 1883952 - 872554 Expected Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5767561 6 chr14 5898046 5902152 - 3141533 7 chr2 9027365 9030522 - 6268365 8 chr2 9027365 9030522 - 9027309 9 chrM 1881625 1883952 - 872554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1rra1yfy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rra1yfy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5769229 7 chr14 5898046 5902152 - 3139336 8 chr2 9027365 9030522 - 6268365 9 chr2 9027365 9030522 - 9027309 13 chrM 1881625 1883952 - 872554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chr14 | 5898046 | 5902152 | a | 0 | ... | | chrM | 1881625 | 1883952 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 9 chrM 1881625 1883952 - 872554 4 chr1 2710326 2711646 - 44860 5 chr1 2710326 2711646 - 2642143 0 chr1 2756505 2765385 - 2688322 1 chr1 2756505 2765385 - 2690968 8 chr14 5898046 5902152 - 3139336 2 chr1 8526271 8532264 - 5763798 3 chr1 8526271 8532264 - 5769229 6 chr2 9027365 9030522 - 6268365 7 chr2 9027365 9030522 - 9027309 df2 Chromosome Start End Strand Distance 13 chrM 1881625 1883952 - 872554 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 7 chr14 5898046 5902152 - 3139336 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5769229 8 chr2 9027365 9030522 - 6268365 9 chr2 9027365 9030522 - 9027309 Actual Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5769229 6 chr14 5898046 5902152 - 3139336 7 chr2 9027365 9030522 - 6268365 8 chr2 9027365 9030522 - 9027309 9 chrM 1881625 1883952 - 872554 Expected Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 44860 1 chr1 2710326 2711646 - 2642143 2 chr1 2756505 2765385 - 2688322 3 chr1 2756505 2765385 - 2690968 4 chr1 8526271 8532264 - 5763798 5 chr1 8526271 8532264 - 5769229 6 chr14 5898046 5902152 - 3139336 7 chr2 9027365 9030522 - 6268365 8 chr2 9027365 9030522 - 9027309 9 chrM 1881625 1883952 - 872554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvsqbc2qb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsqbc2qb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 2703649 1 chr1 2710326 2711646 - 2704176 2 chr1 2756505 2765385 + 2749828 3 chr1 2756505 2765385 + 2750355 4 chr1 8526271 8532264 - 8519594 5 chr1 8526271 8532264 - 8520121 8 chr2 9027365 9030522 - 9024864 12 chrM 1881625 1883952 - 1874274 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 2756505 | 2765385 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 8526271 | 8532264 | a | 0 | ... | | chr1 | 2710326 | 2711646 | a | 0 | ... | | chr1 | 2710326 | 2711646 | a | 0 | ... | | chr2 | 9027365 | 9030522 | a | 0 | ... | | chrM | 1881625 | 1883952 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chrM 1881625 1883952 - 1874274 4 chr1 2710326 2711646 - 2703649 5 chr1 2710326 2711646 - 2704176 0 chr1 2756505 2765385 + 2749828 1 chr1 2756505 2765385 + 2750355 2 chr1 8526271 8532264 - 8519594 3 chr1 8526271 8532264 - 8520121 6 chr2 9027365 9030522 - 9024864 df2 Chromosome Start End Strand Distance 12 chrM 1881625 1883952 - 1874274 0 chr1 2710326 2711646 - 2703649 1 chr1 2710326 2711646 - 2704176 2 chr1 2756505 2765385 + 2749828 3 chr1 2756505 2765385 + 2750355 4 chr1 8526271 8532264 - 8519594 5 chr1 8526271 8532264 - 8520121 8 chr2 9027365 9030522 - 9024864 Actual Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 2703649 1 chr1 2710326 2711646 - 2704176 2 chr1 2756505 2765385 + 2749828 3 chr1 2756505 2765385 + 2750355 4 chr1 8526271 8532264 - 8519594 5 chr1 8526271 8532264 - 8520121 6 chr2 9027365 9030522 - 9024864 7 chrM 1881625 1883952 - 1874274 Expected Chromosome Start End Strand Distance 0 chr1 2710326 2711646 - 2703649 1 chr1 2710326 2711646 - 2704176 2 chr1 2756505 2765385 + 2749828 3 chr1 2756505 2765385 + 2750355 4 chr1 8526271 8532264 - 8519594 5 chr1 8526271 8532264 - 8520121 6 chr2 9027365 9030522 - 9024864 7 chrM 1881625 1883952 - 1874274 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8dxxzpyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8dxxzpyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 65537 71530 - 58860 2 chr1 65537 71530 - 59387 3 chr1 65537 74417 + 58860 4 chr1 65537 74417 + 59387 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 74417 | a | 0 | ... | | chr1 | 65537 | 74417 | a | 0 | ... | | chr1 | 65537 | 71530 | a | 0 | ... | | chr1 | 65537 | 71530 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 65537 71530 - 58860 3 chr1 65537 71530 - 59387 0 chr1 65537 74417 + 58860 1 chr1 65537 74417 + 59387 df2 Chromosome Start End Strand Distance 1 chr1 65537 71530 - 58860 2 chr1 65537 71530 - 59387 3 chr1 65537 74417 + 58860 4 chr1 65537 74417 + 59387 Actual Chromosome Start End Strand Distance 0 chr1 65537 71530 - 58860 1 chr1 65537 71530 - 59387 2 chr1 65537 74417 + 58860 3 chr1 65537 74417 + 59387 Expected Chromosome Start End Strand Distance 0 chr1 65537 71530 - 58860 1 chr1 65537 71530 - 59387 2 chr1 65537 74417 + 58860 3 chr1 65537 74417 + 59387 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9bnh5svd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9bnh5svd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 65537 71530 - 58860 2 chr1 65537 71530 - 59387 3 chr1 65537 74417 + 58860 4 chr1 65537 74417 + 59387 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 74417 | a | 0 | ... | | chr1 | 65537 | 74417 | a | 0 | ... | | chr1 | 65537 | 71530 | a | 0 | ... | | chr1 | 65537 | 71530 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 65537 71530 - 58860 3 chr1 65537 71530 - 59387 0 chr1 65537 74417 + 58860 1 chr1 65537 74417 + 59387 df2 Chromosome Start End Strand Distance 1 chr1 65537 71530 - 58860 2 chr1 65537 71530 - 59387 3 chr1 65537 74417 + 58860 4 chr1 65537 74417 + 59387 Actual Chromosome Start End Strand Distance 0 chr1 65537 71530 - 58860 1 chr1 65537 71530 - 59387 2 chr1 65537 74417 + 58860 3 chr1 65537 74417 + 59387 Expected Chromosome Start End Strand Distance 0 chr1 65537 71530 - 58860 1 chr1 65537 71530 - 59387 2 chr1 65537 74417 + 58860 3 chr1 65537 74417 + 59387 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpidbayk6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidbayk6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 4 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 6 chr1 6939432 6943449 - 2578136 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1553049 | 1557795 | a | 0 | ... | | chr1 | 2796697 | 2804841 | a | 0 | ... | | chr1 | 9252510 | 9259614 | a | 0 | ... | | chr1 | 2963787 | 2965287 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 8894 | a | 0 | ... | | chr1 | 4910128 | 4918617 | a | 0 | ... | | chr1 | 9251337 | 9252190 | a | 0 | ... | | chr1 | 6939432 | 6943449 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 8894 + 9512691 0 chr1 1553049 1557795 + 7963790 1 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 7 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 9 chr1 6939432 6943449 - 2578136 4 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 2 chr1 9252510 9259614 + 261971 df2 Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 4 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 6 chr1 6939432 6943449 - 2578136 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Actual Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 4 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 6 chr1 6939432 6943449 - 2578136 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Expected Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 4 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 6 chr1 6939432 6943449 - 2578136 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb3vfs3tz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3vfs3tz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2052031 2056048 - 7465537 3 chr1 2796697 2804841 + 6716744 4 chr1 2963787 2965287 + 6556298 5 chr1 4910128 4918617 + 4602968 6 chr1 6714337 6723230 + 2798355 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1553049 | 1557795 | a | 0 | ... | | chr1 | 2796697 | 2804841 | a | 0 | ... | | chr1 | 9252510 | 9259614 | a | 0 | ... | | chr1 | 2963787 | 2965287 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 8894 | a | 0 | ... | | chr1 | 4910128 | 4918617 | a | 0 | ... | | chr1 | 9251337 | 9252190 | a | 0 | ... | | chr1 | 2052031 | 2056048 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 8894 + 9512691 0 chr1 1553049 1557795 + 7963790 9 chr1 2052031 2056048 - 7465537 1 chr1 2796697 2804841 + 6716744 3 chr1 2963787 2965287 + 6556298 7 chr1 4910128 4918617 + 4602968 5 chr1 6714337 6723230 + 2798355 4 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 2 chr1 9252510 9259614 + 261971 df2 Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2052031 2056048 - 7465537 3 chr1 2796697 2804841 + 6716744 4 chr1 2963787 2965287 + 6556298 5 chr1 4910128 4918617 + 4602968 6 chr1 6714337 6723230 + 2798355 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Actual Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2052031 2056048 - 7465537 3 chr1 2796697 2804841 + 6716744 4 chr1 2963787 2965287 + 6556298 5 chr1 4910128 4918617 + 4602968 6 chr1 6714337 6723230 + 2798355 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Expected Chromosome Start End Strand Distance 0 chr1 1 8894 + 9512691 1 chr1 1553049 1557795 + 7963790 2 chr1 2052031 2056048 - 7465537 3 chr1 2796697 2804841 + 6716744 4 chr1 2963787 2965287 + 6556298 5 chr1 4910128 4918617 + 4602968 6 chr1 6714337 6723230 + 2798355 7 chr1 8128599 8131307 + 1390278 8 chr1 9251337 9252190 + 269395 9 chr1 9252510 9259614 + 261971 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp22y40lfe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp22y40lfe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppzcnrrxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppzcnrrxt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2419316 | 2427898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 df2 Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 Actual Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 Expected Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmpfnh2xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpfnh2xp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 2353777 1 chr1 2419316 2427898 - 2419310 2 chr1 9521584 9525796 - 9456045 3 chr1 9521584 9525796 - 9521578 4 chr1 9521584 9528114 + 9456045 5 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 8 chr1 9521584 9529908 + 9456045 9 chr1 9521584 9529908 + 9521578 10 chr1 9521584 9530197 + 9456045 11 chr1 9521584 9530197 + 9521578 12 chr16 5424116 5428005 + 5424113 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9521584 | 9528114 | a | 0 | ... | | chr1 | 9521584 | 9528114 | a | 0 | ... | | chr1 | 9521584 | 9530197 | a | 0 | ... | | chr1 | 9521584 | 9530197 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9521584 | 9525796 | a | 0 | ... | | chr1 | 9521584 | 9525796 | a | 0 | ... | | chr1 | 2419316 | 2427898 | a | 0 | ... | | chr1 | 2419316 | 2427898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 2419316 2427898 - 2353777 11 chr1 2419316 2427898 - 2419310 12 chr16 5424116 5428005 + 5424113 8 chr1 9521584 9525796 - 9456045 9 chr1 9521584 9525796 - 9521578 0 chr1 9521584 9528114 + 9456045 1 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 4 chr1 9521584 9529908 + 9456045 5 chr1 9521584 9529908 + 9521578 2 chr1 9521584 9530197 + 9456045 3 chr1 9521584 9530197 + 9521578 df2 Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 2353777 1 chr1 2419316 2427898 - 2419310 12 chr16 5424116 5428005 + 5424113 2 chr1 9521584 9525796 - 9456045 3 chr1 9521584 9525796 - 9521578 4 chr1 9521584 9528114 + 9456045 5 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 8 chr1 9521584 9529908 + 9456045 9 chr1 9521584 9529908 + 9521578 10 chr1 9521584 9530197 + 9456045 11 chr1 9521584 9530197 + 9521578 Actual Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 2353777 1 chr1 2419316 2427898 - 2419310 2 chr1 9521584 9525796 - 9456045 3 chr1 9521584 9525796 - 9521578 4 chr1 9521584 9528114 + 9456045 5 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 8 chr1 9521584 9529908 + 9456045 9 chr1 9521584 9529908 + 9521578 10 chr1 9521584 9530197 + 9456045 11 chr1 9521584 9530197 + 9521578 12 chr16 5424116 5428005 + 5424113 Expected Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 2353777 1 chr1 2419316 2427898 - 2419310 2 chr1 9521584 9525796 - 9456045 3 chr1 9521584 9525796 - 9521578 4 chr1 9521584 9528114 + 9456045 5 chr1 9521584 9528114 + 9521578 6 chr1 9521584 9528166 - 9456045 7 chr1 9521584 9528166 - 9521578 8 chr1 9521584 9529908 + 9456045 9 chr1 9521584 9529908 + 9521578 10 chr1 9521584 9530197 + 9456045 11 chr1 9521584 9530197 + 9521578 12 chr16 5424116 5428005 + 5424113 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpegnnw20a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegnnw20a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 1 chr1 9521584 9525796 - 7093687 2 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 4 chr1 9521584 9529908 + 7093687 5 chr1 9521584 9530197 + 7093687 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9521584 | 9528114 | a | 0 | ... | | chr1 | 9521584 | 9530197 | a | 0 | ... | | chr1 | 9521584 | 9529908 | a | 0 | ... | | chr1 | 9521584 | 9528166 | a | 0 | ... | | chr1 | 9521584 | 9525796 | a | 0 | ... | | chr1 | 2419316 | 2427898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 2419316 2427898 - 7093687 4 chr1 9521584 9525796 - 7093687 0 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 2 chr1 9521584 9529908 + 7093687 1 chr1 9521584 9530197 + 7093687 df2 Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 1 chr1 9521584 9525796 - 7093687 2 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 4 chr1 9521584 9529908 + 7093687 5 chr1 9521584 9530197 + 7093687 Actual Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 1 chr1 9521584 9525796 - 7093687 2 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 4 chr1 9521584 9529908 + 7093687 5 chr1 9521584 9530197 + 7093687 Expected Chromosome Start End Strand Distance 0 chr1 2419316 2427898 - 7093687 1 chr1 9521584 9525796 - 7093687 2 chr1 9521584 9528114 + 7093687 3 chr1 9521584 9528166 - 7093687 4 chr1 9521584 9529908 + 7093687 5 chr1 9521584 9530197 + 7093687 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm31ch_tv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm31ch_tv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 2 chr1 2037311 2038835 + 1858403 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2037311 | 2038835 | a | 0 | ... | | chr1 | 542815 | 542959 | a | 0 | ... | | chr1 | 1 | 10001 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 0 chr1 2037311 2038835 + 1858403 df2 Chromosome Start End Strand Distance 0 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 2 chr1 2037311 2038835 + 1858403 Actual Chromosome Start End Strand Distance 0 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 2 chr1 2037311 2038835 + 1858403 Expected Chromosome Start End Strand Distance 0 chr1 1 10001 + 3887237 1 chr1 542815 542959 + 3354279 2 chr1 2037311 2038835 + 1858403 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb6js16ll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb6js16ll/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 10001 + 532815 1 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 4 chr1 2037311 2038835 + 1494353 5 chr1 2037311 2038835 + 2027311 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2037311 | 2038835 | a | 0 | ... | | chr1 | 2037311 | 2038835 | a | 0 | ... | | chr1 | 542815 | 542959 | a | 0 | ... | | chr1 | 542815 | 542959 | a | 0 | ... | | chr1 | 1 | 10001 | a | 0 | ... | | chr1 | 1 | 10001 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 10001 + 532815 5 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 0 chr1 2037311 2038835 + 1494353 1 chr1 2037311 2038835 + 2027311 df2 Chromosome Start End Strand Distance 0 chr1 1 10001 + 532815 1 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 4 chr1 2037311 2038835 + 1494353 5 chr1 2037311 2038835 + 2027311 Actual Chromosome Start End Strand Distance 0 chr1 1 10001 + 532815 1 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 4 chr1 2037311 2038835 + 1494353 5 chr1 2037311 2038835 + 2027311 Expected Chromosome Start End Strand Distance 0 chr1 1 10001 + 532815 1 chr1 1 10001 + 2027311 2 chr1 542815 542959 + 532815 3 chr1 542815 542959 + 1494353 4 chr1 2037311 2038835 + 1494353 5 chr1 2037311 2038835 + 2027311 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf0mmb0ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0mmb0ox/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 df2 Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6hagcynl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hagcynl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr17 | 4 | 5 | a | 0 | ... | | chr17 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr17 4 5 - 3 4 chr17 4 5 - 7235 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 df2 Chromosome Start End Strand Distance 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 3 chr17 4 5 - 3 4 chr17 4 5 - 7235 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 - 65533 2 chr1 4 5 - 65533 3 chr17 4 5 - 3 4 chr17 4 5 - 7235 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp27px9c53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp27px9c53/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr1 | 4 | 5 | a | 0 | ... | | chr17 | 4 | 5 | a | 0 | ... | | chr17 | 4 | 5 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 df2 Chromosome Start End Strand Distance 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 Actual Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 Expected Chromosome Start End Strand Distance 0 chr1 4 5 + 65533 1 chr1 4 5 + 65533 2 chr1 4 5 - 65533 3 chr1 4 5 - 65533 4 chr17 4 5 - 3 5 chr17 4 5 - 7235 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg8gmrvfx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8gmrvfx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsvkltc15/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvkltc15/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6z338jis/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6z338jis/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 1 chr1 2629111 2634771 + 1014858 2 chr1 2629111 2634771 + 864207 3 chr1 2629111 2634771 + 1014858 4 chr1 2629111 2634771 - 864207 5 chr1 2629111 2634771 - 1014858 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | | chr1 | 2629111 | 2634771 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 2 chr1 2629111 2634771 + 864207 4 chr1 2629111 2634771 - 864207 1 chr1 2629111 2634771 + 1014858 3 chr1 2629111 2634771 + 1014858 5 chr1 2629111 2634771 - 1014858 df2 Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 2 chr1 2629111 2634771 + 864207 4 chr1 2629111 2634771 - 864207 1 chr1 2629111 2634771 + 1014858 3 chr1 2629111 2634771 + 1014858 5 chr1 2629111 2634771 - 1014858 Actual Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 1 chr1 2629111 2634771 + 864207 2 chr1 2629111 2634771 + 1014858 3 chr1 2629111 2634771 + 1014858 4 chr1 2629111 2634771 - 864207 5 chr1 2629111 2634771 - 1014858 Expected Chromosome Start End Strand Distance 0 chr1 2629111 2634771 + 864207 1 chr1 2629111 2634771 + 864207 2 chr1 2629111 2634771 + 1014858 3 chr1 2629111 2634771 + 1014858 4 chr1 2629111 2634771 - 864207 5 chr1 2629111 2634771 - 1014858 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7xwz0o27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xwz0o27/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5660 5662 + 5380 1 chr1 5660 5917 + 5380 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5660 | 5917 | a | 0 | ... | | chr1 | 5660 | 5662 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 5660 5662 + 5380 0 chr1 5660 5917 + 5380 df2 Chromosome Start End Strand Distance 0 chr1 5660 5662 + 5380 1 chr1 5660 5917 + 5380 Actual Chromosome Start End Strand Distance 0 chr1 5660 5662 + 5380 1 chr1 5660 5917 + 5380 Expected Chromosome Start End Strand Distance 0 chr1 5660 5662 + 5380 1 chr1 5660 5917 + 5380 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv14z1ldx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv14z1ldx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65539 + 65257 1 chr1 65537 65794 + 65257 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 65537 65539 + 65257 0 chr1 65537 65794 + 65257 df2 Chromosome Start End Strand Distance 0 chr1 65537 65539 + 65257 1 chr1 65537 65794 + 65257 Actual Chromosome Start End Strand Distance 0 chr1 65537 65539 + 65257 1 chr1 65537 65794 + 65257 Expected Chromosome Start End Strand Distance 0 chr1 65537 65539 + 65257 1 chr1 65537 65794 + 65257 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkhcp1wg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkhcp1wg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 - 60353 4 chr2 65537 65539 - 60353 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 5183 | 5185 | a | 0 | ... | | chr2 | 65537 | 65539 | a | 0 | ... | | chr2 | 65537 | 65539 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 df2 Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 - 60353 4 chr2 65537 65539 - 60353 Actual Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 Expected Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb88kmlu6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb88kmlu6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 - 60353 4 chr2 65537 65539 - 60353 6 chrX 2348 2350 - 63188 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 5183 | 5185 | a | 0 | ... | | chr2 | 65537 | 65539 | a | 0 | ... | | chr2 | 65537 | 65539 | a | 0 | ... | | chrX | 2348 | 2350 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chrX 2348 2350 - 63188 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 df2 Chromosome Start End Strand Distance 6 chrX 2348 2350 - 63188 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 - 60353 4 chr2 65537 65539 - 60353 Actual Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 3 chrX 2348 2350 - 63188 Expected Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 - 60353 2 chr2 65537 65539 - 60353 3 chrX 2348 2350 - 63188 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwssd00k4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwssd00k4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 + 60353 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 65537 | 65539 | a | 0 | ... | | chr2 | 5183 | 5185 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr2 5183 5185 + 60353 0 chr2 65537 65539 + 60353 df2 Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 3 chr2 65537 65539 + 60353 Actual Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 + 60353 Expected Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 1 chr2 65537 65539 + 60353 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7a3n28p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7a3n28p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 5183 | 5185 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 df2 Chromosome Start End Strand Distance 2 chr2 5183 5185 + 60353 Actual Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 Expected Chromosome Start End Strand Distance 0 chr2 5183 5185 + 60353 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjddppi28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjddppi28/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4911929 | 4917782 | a | 0 | ... | | chr1 | 4911929 | 4917782 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 df2 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Actual Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Expected Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbxn9ca1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxn9ca1s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4911929 | 4917782 | a | 0 | ... | | chr1 | 4911929 | 4917782 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 df2 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Actual Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Expected Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4555243 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjg5dii8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjg5dii8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4911929 | 4917782 | a | 0 | ... | | chr1 | 4911929 | 4917782 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 df2 Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 Actual Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 Expected Chromosome Start End Strand Distance 0 chr1 4911929 4917782 + 1903971 1 chr1 4911929 4917782 + 4562513 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ndta1_b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ndta1_b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 349416 | 349417 | a | 0 | ... | | chr1 | 6821752 | 6821753 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 df2 Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 Actual Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 Expected Chromosome Start End Strand Distance 0 chr1 349416 349417 - 6472336 1 chr1 6821752 6821753 - 6472336 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm0eoxlhk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0eoxlhk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 1 chr1 6821752 6821753 - 6821751 2 chr19 9614667 9614668 + 9614666 3 chr8 3816828 3816829 - 3816827 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 349416 | 349417 | a | 0 | ... | | chr1 | 6821752 | 6821753 | a | 0 | ... | | chr8 | 3816828 | 3816829 | a | 0 | ... | | chr19 | 9614667 | 9614668 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 2 chr8 3816828 3816829 - 3816827 1 chr1 6821752 6821753 - 6821751 3 chr19 9614667 9614668 + 9614666 df2 Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 3 chr8 3816828 3816829 - 3816827 1 chr1 6821752 6821753 - 6821751 2 chr19 9614667 9614668 + 9614666 Actual Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 1 chr1 6821752 6821753 - 6821751 2 chr19 9614667 9614668 + 9614666 3 chr8 3816828 3816829 - 3816827 Expected Chromosome Start End Strand Distance 0 chr1 349416 349417 - 349415 1 chr1 6821752 6821753 - 6821751 2 chr19 9614667 9614668 + 9614666 3 chr8 3816828 3816829 - 3816827 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz8pk4g3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8pk4g3j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp63rz8t96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp63rz8t96/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfwcj193/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfwcj193/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4142043 | 4143301 | a | 0 | ... | | chr1 | 4142043 | 4143301 | a | 0 | ... | | chr1 | 1069717 | 1078872 | a | 0 | ... | | chr1 | 1069717 | 1078872 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9521805 | 9529666 | a | 0 | ... | | chr1 | 9521805 | 9529666 | a | 0 | ... | | chr1 | 6132725 | 6136874 | a | 0 | ... | | chr1 | 6132725 | 6136874 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1069717 1078872 - 6981140 3 chr1 1069717 1078872 - 8592821 0 chr1 4142043 4143301 + 3916711 1 chr1 4142043 4143301 + 5528392 6 chr1 4675618 4680602 - 3379410 7 chr1 4675618 4680602 - 4991091 10 chr1 6132725 6136874 - 1923138 11 chr1 6132725 6136874 - 3534819 4 chr1 7175802 7184372 - 875640 5 chr1 7175802 7184372 - 2487321 8 chr1 9521805 9529666 - 142027 9 chr1 9521805 9529666 - 1454608 df2 Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Actual Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Expected Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmd7a9uff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmd7a9uff/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4142043 | 4143301 | a | 0 | ... | | chr1 | 4142043 | 4143301 | a | 0 | ... | | chr1 | 1069717 | 1078872 | a | 0 | ... | | chr1 | 1069717 | 1078872 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9521805 | 9529666 | a | 0 | ... | | chr1 | 9521805 | 9529666 | a | 0 | ... | | chr1 | 6132725 | 6136874 | a | 0 | ... | | chr1 | 6132725 | 6136874 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1069717 1078872 - 6981140 3 chr1 1069717 1078872 - 8592821 0 chr1 4142043 4143301 + 3916711 1 chr1 4142043 4143301 + 5528392 6 chr1 4675618 4680602 - 3379410 7 chr1 4675618 4680602 - 4991091 10 chr1 6132725 6136874 - 1923138 11 chr1 6132725 6136874 - 3534819 4 chr1 7175802 7184372 - 875640 5 chr1 7175802 7184372 - 2487321 8 chr1 9521805 9529666 - 142027 9 chr1 9521805 9529666 - 1454608 df2 Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Actual Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Expected Chromosome Start End Strand Distance 0 chr1 1069717 1078872 - 6981140 1 chr1 1069717 1078872 - 8592821 2 chr1 4142043 4143301 + 3916711 3 chr1 4142043 4143301 + 5528392 4 chr1 4675618 4680602 - 3379410 5 chr1 4675618 4680602 - 4991091 6 chr1 6132725 6136874 - 1923138 7 chr1 6132725 6136874 - 3534819 8 chr1 7175802 7184372 - 875640 9 chr1 7175802 7184372 - 2487321 10 chr1 9521805 9529666 - 142027 11 chr1 9521805 9529666 - 1454608 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7pm_bowa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pm_bowa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1069717 | 1069723 | a | 0 | ... | | chr1 | 1069717 | 1069723 | a | 0 | ... | | chr1 | 4142043 | 4142044 | a | 0 | ... | | chr1 | 4142043 | 4142044 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 6 | a | 0 | ... | | chr1 | 2 | 6 | a | 0 | ... | | chr1 | 6132725 | 6132727 | a | 0 | ... | | chr1 | 6132725 | 6132727 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 2 5 - 65533 7 chr1 2 5 - 8060007 8 chr1 2 6 - 65532 9 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 0 chr1 1069717 1069723 + 1004180 1 chr1 1069717 1069723 + 6990289 2 chr1 4142043 4142044 - 3917968 3 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 df2 Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Actual Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Expected Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbyysqyno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbyysqyno/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1069717 | 1069723 | a | 0 | ... | | chr1 | 1069717 | 1069723 | a | 0 | ... | | chr1 | 4142043 | 4142044 | a | 0 | ... | | chr1 | 4142043 | 4142044 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2 | 6 | a | 0 | ... | | chr1 | 2 | 6 | a | 0 | ... | | chr1 | 6132725 | 6132727 | a | 0 | ... | | chr1 | 6132725 | 6132727 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 2 5 - 65533 7 chr1 2 5 - 8060007 8 chr1 2 6 - 65532 9 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 0 chr1 1069717 1069723 + 1004180 1 chr1 1069717 1069723 + 6990289 2 chr1 4142043 4142044 - 3917968 3 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 df2 Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Actual Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Expected Chromosome Start End Strand Distance 0 chr1 2 5 - 65533 1 chr1 2 5 - 8060007 2 chr1 2 6 - 65532 3 chr1 2 6 - 8060006 4 chr1 5 8 - 65530 5 chr1 5 8 - 8060004 6 chr1 1069717 1069723 + 1004180 7 chr1 1069717 1069723 + 6990289 8 chr1 4142043 4142044 - 3917968 9 chr1 4142043 4142044 - 4076506 10 chr1 6132725 6132727 - 1927285 11 chr1 6132725 6132727 - 6067188 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpew1qa50o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpew1qa50o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 5 2 chr1 5 6 - 1 3 chr1 5 6 - 2 4 chr1 5 7 - 2 5 chr1 5 8 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5 | 6 | a | 0 | ... | | chr1 | 5 | 6 | a | 0 | ... | | chr1 | 5 | 8 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 5 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1 2 - 5 0 chr1 5 6 - 1 1 chr1 5 6 - 2 4 chr1 5 7 - 2 2 chr1 5 8 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 5 2 chr1 5 6 - 1 3 chr1 5 6 - 2 4 chr1 5 7 - 2 5 chr1 5 8 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 5 1 chr1 5 6 - 1 2 chr1 5 6 - 2 3 chr1 5 7 - 2 4 chr1 5 8 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 5 1 chr1 5 6 - 1 2 chr1 5 6 - 2 3 chr1 5 7 - 2 4 chr1 5 8 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpma_yvdnd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpma_yvdnd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 5 2 chr1 5 6 - 1 3 chr1 5 6 - 2 4 chr1 5 7 - 2 5 chr1 5 8 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5 | 6 | a | 0 | ... | | chr1 | 5 | 6 | a | 0 | ... | | chr1 | 5 | 8 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 5 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1 2 - 5 0 chr1 5 6 - 1 1 chr1 5 6 - 2 4 chr1 5 7 - 2 2 chr1 5 8 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 5 2 chr1 5 6 - 1 3 chr1 5 6 - 2 4 chr1 5 7 - 2 5 chr1 5 8 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 5 1 chr1 5 6 - 1 2 chr1 5 6 - 2 3 chr1 5 7 - 2 4 chr1 5 8 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 5 1 chr1 5 6 - 1 2 chr1 5 6 - 2 3 chr1 5 7 - 2 4 chr1 5 8 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxsiqdsh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsiqdsh9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65538 - 65529 4 chr1 65537 65538 - 65534 5 chr1 65537 65542 - 65529 6 chr1 65537 65542 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 65537 65538 - 65529 3 chr1 65537 65538 - 65534 0 chr1 65537 65542 - 65529 1 chr1 65537 65542 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 65537 65538 - 65529 4 chr1 65537 65538 - 65534 5 chr1 65537 65542 - 65529 6 chr1 65537 65542 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65529 1 chr1 65537 65538 - 65534 2 chr1 65537 65542 - 65529 3 chr1 65537 65542 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65529 1 chr1 65537 65538 - 65534 2 chr1 65537 65542 - 65529 3 chr1 65537 65542 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpemaduesg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpemaduesg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10006658 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 df2 Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 Actual Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 Expected Chromosome Start End Strand Distance 0 chr1 10000000 10006658 + 7193284 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphrk23wvi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphrk23wvi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuocutwil/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuocutwil/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqqel4p_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqel4p_v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0izf73n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0izf73n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6x8ln8bo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6x8ln8bo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps6sk_6vk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6sk_6vk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1373867 | 1381103 | a | 0 | ... | | chr1 | 6955840 | 6956918 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 df2 Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 Actual Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 Expected Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 5469886 1 chr1 6955840 6956918 - 98554 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5u4m9cj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5u4m9cj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1373867 | 1381103 | a | 0 | ... | | chr1 | 6955840 | 6956918 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 df2 Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 Actual Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 Expected Chromosome Start End Strand Distance 0 chr1 1373867 1381103 + 1373800 1 chr1 6955840 6956918 - 6955773 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvp5mk8i2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvp5mk8i2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 61 | 5170 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 df2 Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 Actual Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 Expected Chromosome Start End Strand Distance 0 chr1 61 5170 + 60368 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1z7c__pe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1z7c__pe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 106 107 - 65431 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 106 | 107 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 65536 0 chr1 106 107 - 65431 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 106 107 - 65431 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 106 107 - 65431 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 106 107 - 65431 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpikvxl74q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpikvxl74q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsem8xy3w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsem8xy3w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3420973 | a | 0 | ... | | chr1 | 3420790 | 3420973 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3420973 + 338153 1 chr1 3420790 3420973 + 3589185 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmnsi0r7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmnsi0r7w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd537r946/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd537r946/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpehkf8zzm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehkf8zzm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2gcyuo2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gcyuo2c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgx7ueee4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgx7ueee4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3420790 | 3430272 | a | 0 | ... | | chr1 | 3420790 | 3430272 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 df2 Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Expected Chromosome Start End Strand Distance 0 chr1 3420790 3430272 - 3354997 1 chr1 3420790 3430272 - 3420454 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9k92xs9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9k92xs9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 80 337 + 65201 1 chr1 65537 65794 + 65201 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 80 | 337 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 80 337 + 65201 0 chr1 65537 65794 + 65201 df2 Chromosome Start End Strand Distance 0 chr1 80 337 + 65201 1 chr1 65537 65794 + 65201 Actual Chromosome Start End Strand Distance 0 chr1 80 337 + 65201 1 chr1 65537 65794 + 65201 Expected Chromosome Start End Strand Distance 0 chr1 80 337 + 65201 1 chr1 65537 65794 + 65201 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm53qp1yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm53qp1yv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 557234 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 8 chr17 4069990 4079662 - 3688711 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4437037 | 4438637 | a | 0 | ... | | chr1 | 4437037 | 4438637 | a | 0 | ... | | chr1 | 9149560 | 9151160 | a | 0 | ... | | chr1 | 9149560 | 9151160 | a | 0 | ... | | chr1 | 4816435 | 4818035 | a | 0 | ... | | chr1 | 4816435 | 4818035 | a | 0 | ... | | chr13 | 282116 | 283716 | a | 0 | ... | | chr17 | 4069990 | 4079662 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 4 chr1 4816435 4818035 - 204998 5 chr1 4816435 4818035 - 557234 2 chr1 9149560 9151160 - 579776 3 chr1 9149560 9151160 - 4119439 df2 Chromosome Start End Strand Distance 6 chr13 282116 283716 + 2483040 8 chr17 4069990 4079662 - 3688711 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 557234 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 Actual Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 557234 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 Expected Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 177836 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 557234 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvhpzy772/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvhpzy772/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 560011 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 8 chr17 4069990 4079662 - 3688711 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4437037 | 4438637 | a | 0 | ... | | chr1 | 4437037 | 4438637 | a | 0 | ... | | chr1 | 9149560 | 9151160 | a | 0 | ... | | chr1 | 9149560 | 9151160 | a | 0 | ... | | chr1 | 4816435 | 4818035 | a | 0 | ... | | chr1 | 4816435 | 4818035 | a | 0 | ... | | chr13 | 282116 | 283716 | a | 0 | ... | | chr17 | 4069990 | 4079662 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 4 chr1 4816435 4818035 - 204998 5 chr1 4816435 4818035 - 560011 2 chr1 9149560 9151160 - 579776 3 chr1 9149560 9151160 - 4119439 df2 Chromosome Start End Strand Distance 6 chr13 282116 283716 + 2483040 8 chr17 4069990 4079662 - 3688711 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 560011 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 Actual Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 560011 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 Expected Chromosome Start End Strand Distance 0 chr1 4437037 4438637 + 180613 1 chr1 4437037 4438637 + 584396 2 chr1 4816435 4818035 - 204998 3 chr1 4816435 4818035 - 560011 4 chr1 9149560 9151160 - 579776 5 chr1 9149560 9151160 - 4119439 6 chr13 282116 283716 + 2483040 7 chr17 4069990 4079662 - 3688711 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps58azpgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps58azpgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 4092 - 1383881 1 chr1 2 4092 - 3398906 2 chr1 1387972 1395206 - 1383881 3 chr1 1387972 1395206 - 2007792 4 chr1 3402997 3412438 + 838683 5 chr1 3402997 3412438 + 1610595 6 chr1 4251120 4256425 - 766608 7 chr1 4251120 4256425 - 838683 8 chr1 5023032 5030122 + 766608 9 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5023032 | 5030122 | a | 0 | ... | | chr1 | 5023032 | 5030122 | a | 0 | ... | | chr1 | 3402997 | 3412438 | a | 0 | ... | | chr1 | 3402997 | 3412438 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1387972 | 1395206 | a | 0 | ... | | chr1 | 1387972 | 1395206 | a | 0 | ... | | chr1 | 9730935 | 9734072 | a | 0 | ... | | chr1 | 9730935 | 9734072 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 2 4092 - 1383881 7 chr1 2 4092 - 3398906 8 chr1 1387972 1395206 - 1383881 9 chr1 1387972 1395206 - 2007792 2 chr1 3402997 3412438 + 838683 3 chr1 3402997 3412438 + 1610595 4 chr1 4251120 4256425 - 766608 5 chr1 4251120 4256425 - 838683 0 chr1 5023032 5030122 + 766608 1 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 df2 Chromosome Start End Strand Distance 0 chr1 2 4092 - 1383881 1 chr1 2 4092 - 3398906 2 chr1 1387972 1395206 - 1383881 3 chr1 1387972 1395206 - 2007792 4 chr1 3402997 3412438 + 838683 5 chr1 3402997 3412438 + 1610595 6 chr1 4251120 4256425 - 766608 7 chr1 4251120 4256425 - 838683 8 chr1 5023032 5030122 + 766608 9 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 Actual Chromosome Start End Strand Distance 0 chr1 2 4092 - 1383881 1 chr1 2 4092 - 3398906 2 chr1 1387972 1395206 - 1383881 3 chr1 1387972 1395206 - 2007792 4 chr1 3402997 3412438 + 838683 5 chr1 3402997 3412438 + 1610595 6 chr1 4251120 4256425 - 766608 7 chr1 4251120 4256425 - 838683 8 chr1 5023032 5030122 + 766608 9 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 Expected Chromosome Start End Strand Distance 0 chr1 2 4092 - 1383881 1 chr1 2 4092 - 3398906 2 chr1 1387972 1395206 - 1383881 3 chr1 1387972 1395206 - 2007792 4 chr1 3402997 3412438 + 838683 5 chr1 3402997 3412438 + 1610595 6 chr1 4251120 4256425 - 766608 7 chr1 4251120 4256425 - 838683 8 chr1 5023032 5030122 + 766608 9 chr1 5023032 5030122 + 1610595 10 chr1 9730935 9734072 - 4700814 11 chr1 9730935 9734072 - 5474511 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4tmfdppz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4tmfdppz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3137 6274 - 1381699 1 chr1 3137 6274 - 3396724 2 chr1 4090 8180 - 1379793 3 chr1 4090 8180 - 3394818 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 6 chr1 7090 14180 + 2999 7 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 10 chr1 9441 18882 + 5350 11 chr1 9441 18882 + 1369091 12 chr11 10000000 10010000 + 8161694 13 chr13 2887 5774 - 2760982 14 chr17 4608 9216 - 367457 15 chr22 7243 14486 + 6606587 16 chr6 8488 16976 - 8607893 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7090 | 14180 | a | 0 | ... | | chr1 | 7090 | 14180 | a | 0 | ... | | chr1 | 9441 | 18882 | a | 0 | ... | | chr1 | 9441 | 18882 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr11 | 10000000 | 10010000 | a | 0 | ... | | chr13 | 2887 | 5774 | a | 0 | ... | | chr17 | 4608 | 9216 | a | 0 | ... | | chr22 | 7243 | 14486 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 14 chr13 2887 5774 - 2760982 10 chr1 3137 6274 - 1381699 11 chr1 3137 6274 - 3396724 6 chr1 4090 8180 - 1379793 7 chr1 4090 8180 - 3394818 15 chr17 4608 9216 - 367457 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 0 chr1 7090 14180 + 2999 1 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 16 chr22 7243 14486 + 6606587 12 chr6 8488 16976 - 8607893 2 chr1 9441 18882 + 5350 3 chr1 9441 18882 + 1369091 13 chr11 10000000 10010000 + 8161694 df2 Chromosome Start End Strand Distance 13 chr13 2887 5774 - 2760982 0 chr1 3137 6274 - 1381699 1 chr1 3137 6274 - 3396724 2 chr1 4090 8180 - 1379793 3 chr1 4090 8180 - 3394818 14 chr17 4608 9216 - 367457 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 6 chr1 7090 14180 + 2999 7 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 15 chr22 7243 14486 + 6606587 16 chr6 8488 16976 - 8607893 10 chr1 9441 18882 + 5350 11 chr1 9441 18882 + 1369091 12 chr11 10000000 10010000 + 8161694 Actual Chromosome Start End Strand Distance 0 chr1 3137 6274 - 1381699 1 chr1 3137 6274 - 3396724 2 chr1 4090 8180 - 1379793 3 chr1 4090 8180 - 3394818 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 6 chr1 7090 14180 + 2999 7 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 10 chr1 9441 18882 + 5350 11 chr1 9441 18882 + 1369091 12 chr11 10000000 10010000 + 8161694 13 chr13 2887 5774 - 2760982 14 chr17 4608 9216 - 367457 15 chr22 7243 14486 + 6606587 16 chr6 8488 16976 - 8607893 Expected Chromosome Start End Strand Distance 0 chr1 3137 6274 - 1381699 1 chr1 3137 6274 - 3396724 2 chr1 4090 8180 - 1379793 3 chr1 4090 8180 - 3394818 4 chr1 5305 10610 - 1214 5 chr1 5305 10610 - 1377363 6 chr1 7090 14180 + 2999 7 chr1 7090 14180 + 1373793 8 chr1 7234 14468 - 3143 9 chr1 7234 14468 - 1373505 10 chr1 9441 18882 + 5350 11 chr1 9441 18882 + 1369091 12 chr11 10000000 10010000 + 8161694 13 chr13 2887 5774 - 2760982 14 chr17 4608 9216 - 367457 15 chr22 7243 14486 + 6606587 16 chr6 8488 16976 - 8607893 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwuhinvce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwuhinvce/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10 12 + 7 1 chr1 10 12 + 65526 2 chr1 10 12 - 7 3 chr1 10 12 - 65526 4 chr1 4090 4092 - 4078 5 chr1 4090 4092 - 4087 6 chr1 9441 9443 - 9429 7 chr1 9441 9443 - 9438 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10 | 12 | a | 0 | ... | | chr1 | 10 | 12 | a | 0 | ... | | chr1 | 10 | 12 | a | 0 | ... | | chr1 | 10 | 12 | a | 0 | ... | | chr1 | 9441 | 9443 | a | 0 | ... | | chr1 | 9441 | 9443 | a | 0 | ... | | chr1 | 4090 | 4092 | a | 0 | ... | | chr1 | 4090 | 4092 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 10 12 + 7 2 chr1 10 12 - 7 1 chr1 10 12 + 65526 3 chr1 10 12 - 65526 6 chr1 4090 4092 - 4078 7 chr1 4090 4092 - 4087 4 chr1 9441 9443 - 9429 5 chr1 9441 9443 - 9438 df2 Chromosome Start End Strand Distance 0 chr1 10 12 + 7 2 chr1 10 12 - 7 1 chr1 10 12 + 65526 3 chr1 10 12 - 65526 4 chr1 4090 4092 - 4078 5 chr1 4090 4092 - 4087 6 chr1 9441 9443 - 9429 7 chr1 9441 9443 - 9438 Actual Chromosome Start End Strand Distance 0 chr1 10 12 + 7 1 chr1 10 12 + 65526 2 chr1 10 12 - 7 3 chr1 10 12 - 65526 4 chr1 4090 4092 - 4078 5 chr1 4090 4092 - 4087 6 chr1 9441 9443 - 9429 7 chr1 9441 9443 - 9438 Expected Chromosome Start End Strand Distance 0 chr1 10 12 + 7 1 chr1 10 12 + 65526 2 chr1 10 12 - 7 3 chr1 10 12 - 65526 4 chr1 4090 4092 - 4078 5 chr1 4090 4092 - 4087 6 chr1 9441 9443 - 9429 7 chr1 9441 9443 - 9438 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpauqi4cei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpauqi4cei/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 9441 9443 - 9405 2 chr1 9441 9443 - 9436 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9441 | 9443 | a | 0 | ... | | chr1 | 9441 | 9443 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9441 9443 - 9405 1 chr1 9441 9443 - 9436 df2 Chromosome Start End Strand Distance 1 chr1 9441 9443 - 9405 2 chr1 9441 9443 - 9436 Actual Chromosome Start End Strand Distance 0 chr1 9441 9443 - 9405 1 chr1 9441 9443 - 9436 Expected Chromosome Start End Strand Distance 0 chr1 9441 9443 - 9405 1 chr1 9441 9443 - 9436 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5cqnml5b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5cqnml5b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa4cwomxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4cwomxv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 893138 900766 - 8252862 1 chr1 1977785 1980587 - 7173041 2 chr1 2137836 2141603 + 7012025 3 chr1 3011321 3015378 - 6138250 4 chr1 3011321 3017780 - 6135848 5 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 7 chr1 6038708 6042886 - 3110742 8 chr1 7061761 7070084 + 2083544 9 chr1 7418574 7419400 + 1734228 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7061761 | 7070084 | a | 0 | ... | | chr1 | 2137836 | 2141603 | a | 0 | ... | | chr1 | 7418574 | 7419400 | a | 0 | ... | | chr1 | 4585257 | 4586204 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5608261 | 5613316 | a | 0 | ... | | chr1 | 1977785 | 1980587 | a | 0 | ... | | chr1 | 3011321 | 3017780 | a | 0 | ... | | chr1 | 3011321 | 3015378 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 893138 900766 - 8252862 7 chr1 1977785 1980587 - 7173041 1 chr1 2137836 2141603 + 7012025 9 chr1 3011321 3015378 - 6138250 8 chr1 3011321 3017780 - 6135848 3 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 5 chr1 6038708 6042886 - 3110742 0 chr1 7061761 7070084 + 2083544 2 chr1 7418574 7419400 + 1734228 df2 Chromosome Start End Strand Distance 0 chr1 893138 900766 - 8252862 1 chr1 1977785 1980587 - 7173041 2 chr1 2137836 2141603 + 7012025 3 chr1 3011321 3015378 - 6138250 4 chr1 3011321 3017780 - 6135848 5 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 7 chr1 6038708 6042886 - 3110742 8 chr1 7061761 7070084 + 2083544 9 chr1 7418574 7419400 + 1734228 Actual Chromosome Start End Strand Distance 0 chr1 893138 900766 - 8252862 1 chr1 1977785 1980587 - 7173041 2 chr1 2137836 2141603 + 7012025 3 chr1 3011321 3015378 - 6138250 4 chr1 3011321 3017780 - 6135848 5 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 7 chr1 6038708 6042886 - 3110742 8 chr1 7061761 7070084 + 2083544 9 chr1 7418574 7419400 + 1734228 Expected Chromosome Start End Strand Distance 0 chr1 893138 900766 - 8252862 1 chr1 1977785 1980587 - 7173041 2 chr1 2137836 2141603 + 7012025 3 chr1 3011321 3015378 - 6138250 4 chr1 3011321 3017780 - 6135848 5 chr1 4585257 4586204 + 4567424 6 chr1 5608261 5613316 - 3540312 7 chr1 6038708 6042886 - 3110742 8 chr1 7061761 7070084 + 2083544 9 chr1 7418574 7419400 + 1734228 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3vuqjtmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vuqjtmv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7c0p289_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7c0p289_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2615129 2621642 + 2933057 3 chr1 2615129 2621642 + 7378359 8 chr1 5093094 5099699 - 455000 9 chr1 5093094 5099699 - 4900302 10 chr1 5532278 5536581 - 18118 11 chr1 5532278 5536581 - 4463420 0 chr1 7225386 7233529 + 1668099 1 chr1 7225386 7233529 + 2766472 6 chr1 8135388 8138430 - 1861571 7 chr1 8135388 8138430 - 2578101 12 chr1 8254305 8261673 - 1738328 13 chr1 8254305 8261673 - 2697018 4 chr1 9140426 9150079 + 849922 5 chr1 9140426 9150079 + 3583139 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqxy4vx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqxy4vx9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2615129 2621642 + 2933057 3 chr1 2615129 2621642 + 7378359 8 chr1 5093094 5099699 - 455000 9 chr1 5093094 5099699 - 4900302 10 chr1 5532278 5536581 - 18118 11 chr1 5532278 5536581 - 4463420 0 chr1 7225386 7233529 + 1668099 1 chr1 7225386 7233529 + 2766472 6 chr1 8135388 8138430 - 1861571 7 chr1 8135388 8138430 - 2578101 12 chr1 8254305 8261673 - 1738328 13 chr1 8254305 8261673 - 2697018 4 chr1 9140426 9150079 + 849922 5 chr1 9140426 9150079 + 3583139 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6mih4ewx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mih4ewx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | | chr1 | 8254305 | 8261673 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2615129 2621642 + 2933057 3 chr1 2615129 2621642 + 7378359 8 chr1 5093094 5099699 - 455000 9 chr1 5093094 5099699 - 4900302 10 chr1 5532278 5536581 - 18118 11 chr1 5532278 5536581 - 4463420 0 chr1 7225386 7233529 + 1668099 1 chr1 7225386 7233529 + 2766472 6 chr1 8135388 8138430 - 1861571 7 chr1 8135388 8138430 - 2578101 12 chr1 8254305 8261673 - 1738328 13 chr1 8254305 8261673 - 2697018 4 chr1 9140426 9150079 + 849922 5 chr1 9140426 9150079 + 3583139 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 + 2933057 1 chr1 2615129 2621642 + 7378359 2 chr1 5093094 5099699 - 455000 3 chr1 5093094 5099699 - 4900302 4 chr1 5532278 5536581 - 18118 5 chr1 5532278 5536581 - 4463420 6 chr1 7225386 7233529 + 1668099 7 chr1 7225386 7233529 + 2766472 8 chr1 8135388 8138430 - 1861571 9 chr1 8135388 8138430 - 2578101 10 chr1 8254305 8261673 - 1738328 11 chr1 8254305 8261673 - 2697018 12 chr1 9140426 9150079 + 849922 13 chr1 9140426 9150079 + 3583139 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5dxsb709/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5dxsb709/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 - 5466741 5 chr1 5532278 5536581 - 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 8135388 | 8138430 | a | 0 | ... | | chr1 | 8135388 | 8138430 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5093094 | 5099699 | a | 0 | ... | | chr1 | 5093094 | 5099699 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | | chr1 | 5532278 | 5536581 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 2615129 2621642 - 2549592 9 chr1 2615129 2621642 - 2614872 10 chr1 5093094 5099699 - 5027557 11 chr1 5093094 5099699 - 5092837 12 chr1 5532278 5536581 - 5466741 13 chr1 5532278 5536581 - 5532021 0 chr1 7225386 7233529 + 7159849 1 chr1 7225386 7233529 + 7225129 2 chr1 8135388 8138430 + 8069851 3 chr1 8135388 8138430 + 8135131 6 chr1 8254305 8261673 + 8188768 7 chr1 8254305 8261673 + 8254048 4 chr1 9140426 9150079 + 9074889 5 chr1 9140426 9150079 + 9140169 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 - 5466741 5 chr1 5532278 5536581 - 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 - 5466741 5 chr1 5532278 5536581 - 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 - 5466741 5 chr1 5532278 5536581 - 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5k8z5_y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5k8z5_y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 7225386 | 7233529 | a | 0 | ... | | chr1 | 8135388 | 8138430 | a | 0 | ... | | chr1 | 8135388 | 8138430 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 2615129 | 2621642 | a | 0 | ... | | chr1 | 5093094 | 5099699 | a | 0 | ... | | chr1 | 5093094 | 5099699 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 14 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 2615129 2621642 - 2549592 11 chr1 2615129 2621642 - 2614872 12 chr1 5093094 5099699 - 5027557 13 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 0 chr1 7225386 7233529 + 7159849 1 chr1 7225386 7233529 + 7225129 2 chr1 8135388 8138430 + 8069851 3 chr1 8135388 8138430 + 8135131 8 chr1 8254305 8261673 + 8188768 9 chr1 8254305 8261673 + 8254048 6 chr1 9140426 9150079 + 9074889 7 chr1 9140426 9150079 + 9140169 df2 Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Actual Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Expected Chromosome Start End Strand Distance 0 chr1 2615129 2621642 - 2549592 1 chr1 2615129 2621642 - 2614872 2 chr1 5093094 5099699 - 5027557 3 chr1 5093094 5099699 - 5092837 4 chr1 5532278 5536581 + 5466741 5 chr1 5532278 5536581 + 5532021 6 chr1 7225386 7233529 + 7159849 7 chr1 7225386 7233529 + 7225129 8 chr1 8135388 8138430 + 8069851 9 chr1 8135388 8138430 + 8135131 10 chr1 8254305 8261673 + 8188768 11 chr1 8254305 8261673 + 8254048 12 chr1 9140426 9150079 + 9074889 13 chr1 9140426 9150079 + 9140169 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=14, step=1) Expected index RangeIndex(start=0, stop=14, step=1) index equal [ True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkj9cv030/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkj9cv030/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 65537 65542 - 56211 4 chr1 65537 65542 - 65532 5 chr1 2615129 2615134 - 2605803 6 chr1 2615129 2615134 - 2615124 7 chr1 8135388 8135393 - 8126062 8 chr1 8135388 8135393 - 8135383 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8135388 | 8135393 | a | 0 | ... | | chr1 | 8135388 | 8135393 | a | 0 | ... | | chr1 | 2615129 | 2615134 | a | 0 | ... | | chr1 | 2615129 | 2615134 | a | 0 | ... | | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65542 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 65537 65542 - 56211 5 chr1 65537 65542 - 65532 2 chr1 2615129 2615134 - 2605803 3 chr1 2615129 2615134 - 2615124 0 chr1 8135388 8135393 - 8126062 1 chr1 8135388 8135393 - 8135383 df2 Chromosome Start End Strand Distance 3 chr1 65537 65542 - 56211 4 chr1 65537 65542 - 65532 5 chr1 2615129 2615134 - 2605803 6 chr1 2615129 2615134 - 2615124 7 chr1 8135388 8135393 - 8126062 8 chr1 8135388 8135393 - 8135383 Actual Chromosome Start End Strand Distance 0 chr1 65537 65542 - 56211 1 chr1 65537 65542 - 65532 2 chr1 2615129 2615134 - 2605803 3 chr1 2615129 2615134 - 2615124 4 chr1 8135388 8135393 - 8126062 5 chr1 8135388 8135393 - 8135383 Expected Chromosome Start End Strand Distance 0 chr1 65537 65542 - 56211 1 chr1 65537 65542 - 65532 2 chr1 2615129 2615134 - 2605803 3 chr1 2615129 2615134 - 2615124 4 chr1 8135388 8135393 - 8126062 5 chr1 8135388 8135393 - 8135383 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvsu86_n0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsu86_n0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65512 1 chr1 65537 65538 - 65512 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65542 + 65512 5 chr1 65537 65794 - 65512 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65542 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65538 - 65512 5 chr1 65537 65538 - 65512 0 chr1 65537 65542 + 65512 1 chr1 65537 65794 - 65512 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65512 1 chr1 65537 65538 - 65512 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65542 + 65512 5 chr1 65537 65794 - 65512 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65512 1 chr1 65537 65538 - 65512 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65542 + 65512 5 chr1 65537 65794 - 65512 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65512 1 chr1 65537 65538 - 65512 2 chr1 65537 65538 - 65512 3 chr1 65537 65538 - 65512 4 chr1 65537 65542 + 65512 5 chr1 65537 65794 - 65512 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7nmlzxuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nmlzxuc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 428464 | 433767 | a | 0 | ... | | chr1 | 4109934 | 4118195 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 df2 Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 Actual Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 Expected Chromosome Start End Strand Distance 0 chr1 428464 433767 + 3109155 1 chr1 4109934 4118195 + 557240 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppjnioyqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppjnioyqd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr10 6122965 6130048 + 2570271 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr10 | 6122965 | 6130048 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr10 6122965 6130048 + 2570271 df2 Chromosome Start End Strand Distance 2 chr10 6122965 6130048 + 2570271 Actual Chromosome Start End Strand Distance 0 chr10 6122965 6130048 + 2570271 Expected Chromosome Start End Strand Distance 0 chr10 6122965 6130048 + 2570271 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnln66alb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnln66alb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpold6k63h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpold6k63h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9kjc0fj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9kjc0fj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3px2hz_0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3px2hz_0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj2vn9mc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2vn9mc5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbmvy4u5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmvy4u5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1894566 1895027 - 1771318 1 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 4 chr1 7774529 7776683 + 732921 5 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 8 chr1 9999999 10002153 - 962584 9 chr1 9999999 10002153 - 2958391 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7774529 | 7776683 | a | 0 | ... | | chr1 | 7774529 | 7776683 | a | 0 | ... | | chr1 | 7757937 | 7767509 | a | 0 | ... | | chr1 | 7757937 | 7767509 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 7835770 | 7839870 | a | 0 | ... | | chr1 | 7835770 | 7839870 | a | 0 | ... | | chr1 | 1894566 | 1895027 | a | 0 | ... | | chr1 | 1894566 | 1895027 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 8 chr1 1894566 1895027 - 1771318 9 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 0 chr1 7774529 7776683 + 732921 1 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 4 chr1 9999999 10002153 - 962584 5 chr1 9999999 10002153 - 2958391 df2 Chromosome Start End Strand Distance 0 chr1 1894566 1895027 - 1771318 1 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 4 chr1 7774529 7776683 + 732921 5 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 8 chr1 9999999 10002153 - 962584 9 chr1 9999999 10002153 - 2958391 Actual Chromosome Start End Strand Distance 0 chr1 1894566 1895027 - 1771318 1 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 4 chr1 7774529 7776683 + 732921 5 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 8 chr1 9999999 10002153 - 962584 9 chr1 9999999 10002153 - 2958391 Expected Chromosome Start End Strand Distance 0 chr1 1894566 1895027 - 1771318 1 chr1 1894566 1895027 - 3011929 2 chr1 7757937 7767509 + 716329 3 chr1 7757937 7767509 + 1264334 4 chr1 7774529 7776683 + 732921 5 chr1 7774529 7776683 + 1255160 6 chr1 7835770 7839870 - 794162 7 chr1 7835770 7839870 - 1191973 8 chr1 9999999 10002153 - 962584 9 chr1 9999999 10002153 - 2958391 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwe5ctwxy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwe5ctwxy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7774529 7774786 - 7774519 3 chr1 7835770 7836027 - 7835760 4 chr1 9999999 10000256 - 9999989 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7774529 | 7774786 | a | 0 | ... | | chr1 | 9999999 | 10000256 | a | 0 | ... | | chr1 | 7835770 | 7836027 | a | 0 | ... | | chr1 | 7757937 | 7758194 | a | 0 | ... | | chr1 | 1894566 | 1894823 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1894566 1894823 - 1894556 3 chr1 7757937 7758194 - 7757927 0 chr1 7774529 7774786 - 7774519 2 chr1 7835770 7836027 - 7835760 1 chr1 9999999 10000256 - 9999989 df2 Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7774529 7774786 - 7774519 3 chr1 7835770 7836027 - 7835760 4 chr1 9999999 10000256 - 9999989 Actual Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7774529 7774786 - 7774519 3 chr1 7835770 7836027 - 7835760 4 chr1 9999999 10000256 - 9999989 Expected Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7774529 7774786 - 7774519 3 chr1 7835770 7836027 - 7835760 4 chr1 9999999 10000256 - 9999989 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe261jo8u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe261jo8u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 3 chr1 9399417 9399674 - 9399407 4 chr1 9999999 10000256 - 9999989 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9399417 | 9399674 | a | 0 | ... | | chr1 | 9999999 | 10000256 | a | 0 | ... | | chr1 | 7835770 | 7836027 | a | 0 | ... | | chr1 | 7757937 | 7758194 | a | 0 | ... | | chr1 | 1894566 | 1894823 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1894566 1894823 - 1894556 3 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 0 chr1 9399417 9399674 - 9399407 1 chr1 9999999 10000256 - 9999989 df2 Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 3 chr1 9399417 9399674 - 9399407 4 chr1 9999999 10000256 - 9999989 Actual Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 3 chr1 9399417 9399674 - 9399407 4 chr1 9999999 10000256 - 9999989 Expected Chromosome Start End Strand Distance 0 chr1 1894566 1894823 - 1894556 1 chr1 7757937 7758194 - 7757927 2 chr1 7835770 7836027 - 7835760 3 chr1 9399417 9399674 - 9399407 4 chr1 9999999 10000256 - 9999989 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyazptldz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyazptldz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65527 1 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 3 chr1 9999999 10000256 - 9999989 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9999999 | 10000256 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 7757937 | 7758194 | a | 0 | ... | | chr1 | 1894566 | 1894823 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 65537 65794 - 65527 3 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 0 chr1 9999999 10000256 - 9999989 df2 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65527 1 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 3 chr1 9999999 10000256 - 9999989 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65527 1 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 3 chr1 9999999 10000256 - 9999989 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65527 1 chr1 1894566 1894823 - 1894556 2 chr1 7757937 7758194 - 7757927 3 chr1 9999999 10000256 - 9999989 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2fga1zs_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2fga1zs_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr3 | 2684509 | 2691332 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 df2 Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Actual Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Expected Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn7vkwqyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7vkwqyn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr3 | 2684509 | 2691332 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 df2 Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Actual Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Expected Chromosome Start End Strand Distance 0 chr3 2684509 2691332 - 262773 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp1orupya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1orupya/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6i_76cg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6i_76cg6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3dcy9juz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3dcy9juz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4177261 | 4184084 | a | 0 | ... | | chr1 | 4177261 | 4184084 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 df2 Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 Actual Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 Expected Chromosome Start End Strand Distance 0 chr1 4177261 4184084 - 4176999 1 chr1 4177261 4184084 - 4177003 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcihf6sjp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcihf6sjp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpot1t3u5u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpot1t3u5u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi8_kb4c4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8_kb4c4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzcuxlu6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzcuxlu6r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4pkyqoay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4pkyqoay/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 + 2 4 chr1 3 6 + 2 5 chr1 3 7 + 1 6 chr1 3 7 + 2 0 chr1 3 1284 + 2 1 chr1 97 104 + 90 2 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 0 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 6 + 2 2 chr1 3 7 + 1 3 chr1 3 7 + 2 4 chr1 3 1284 + 2 5 chr1 97 104 + 90 6 chr1 97 104 + 96 7 chr1 65537 65540 - 65274 8 chr1 65537 65540 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 + 2 1 chr1 3 7 + 1 2 chr1 3 7 + 2 3 chr1 3 1284 + 2 4 chr1 97 104 + 90 5 chr1 97 104 + 96 6 chr1 65537 65540 - 65274 7 chr1 65537 65540 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1tyvb96j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1tyvb96j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 6 - 2 2 chr1 3 7 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 5 chr1 65537 65540 + 65533 6 chr1 65537 65540 + 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 3 6 - 2 6 chr1 3 7 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 0 chr1 65537 65540 + 65533 1 chr1 65537 65540 + 65536 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 7 - 2 0 chr1 3 1284 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 5 chr1 65537 65540 + 65533 6 chr1 65537 65540 + 65536 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 7 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 5 chr1 65537 65540 + 65533 6 chr1 65537 65540 + 65536 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 7 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 93 4 chr1 97 104 - 96 5 chr1 65537 65540 + 65533 6 chr1 65537 65540 + 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbd6vzcnk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbd6vzcnk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 97 100 - 96 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 100 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 100 - 96 df2 Chromosome Start End Strand Distance 4 chr1 97 100 - 96 Actual Chromosome Start End Strand Distance 0 chr1 97 100 - 96 Expected Chromosome Start End Strand Distance 0 chr1 97 100 - 96 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplqv7txog/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqv7txog/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 9 | a | 0 | ... | | chr1 | 3 | 9 | a | 0 | ... | | chr1 | 3 | 9 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 65537 | 65543 | a | 0 | ... | | chr1 | 65537 | 65543 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 df2 Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 9 + 2 1 chr1 3 9 + 2 2 chr1 3 9 + 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65543 - 65274 6 chr1 65537 65543 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qj5zfy0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qj5zfy0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 6 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 4 chr1 3 6 - 2 0 chr1 3 1284 - 2 7 chr1 3 1284 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 1284 - 2 3 chr1 3 1284 - 2 4 chr1 97 104 - 90 5 chr1 97 104 - 96 6 chr1 65537 66818 - 65274 7 chr1 65537 66818 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnojrjshb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnojrjshb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 4 chr1 3 6 - 2 7 chr1 3 260 - 2 0 chr1 3 1284 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 260 - 2 0 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 1284 - 2 4 chr1 97 104 - 90 5 chr1 97 104 - 96 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_r_aibpw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_r_aibpw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 3 chr1 3 1284 - 2 6 chr1 3 1284 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 4 chr1 65537 66818 - 65274 5 chr1 65537 66818 - 65530 df2 Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplsqu41zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplsqu41zj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 2 chr1 3 6 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 1284 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 65537 | 66818 | a | 0 | ... | | chr1 | 3 | 1284 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 4 chr1 3 6 - 2 0 chr1 3 1284 - 2 7 chr1 3 1284 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 0 chr1 3 1284 - 2 1 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 1284 - 2 3 chr1 3 1284 - 2 4 chr1 97 104 - 90 5 chr1 97 104 - 96 6 chr1 65537 66818 - 65274 7 chr1 65537 66818 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 1284 - 2 2 chr1 3 1284 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 66818 - 65274 6 chr1 65537 66818 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5o19k841/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5o19k841/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 65537 66818 + 65280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 66818 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 66818 + 65280 df2 Chromosome Start End Strand Distance 4 chr1 65537 66818 + 65280 Actual Chromosome Start End Strand Distance 0 chr1 65537 66818 + 65280 Expected Chromosome Start End Strand Distance 0 chr1 65537 66818 + 65280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphcjbyggl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcjbyggl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 97 104 - 94 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 97 104 - 94 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgfq1t095/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfq1t095/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 4 chr1 3 6 - 2 0 chr1 3 260 - 2 7 chr1 3 260 - 2 1 chr1 97 104 - 90 2 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 0 chr1 3 260 - 2 1 chr1 3 260 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 97 104 - 90 5 chr1 97 104 - 96 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 97 104 - 90 4 chr1 97 104 - 96 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp48dqbaae/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp48dqbaae/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpct1fsxf1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpct1fsxf1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 97 104 - 94 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 104 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 97 104 - 94 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 104 - 94 1 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwki_0gef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwki_0gef/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 97 98 - 94 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 98 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 97 98 - 94 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprzugkoid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzugkoid/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 97 98 - 94 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 97 | 98 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 3 chr1 97 98 - 94 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz4ncki89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4ncki89/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 97 | 98 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 97 98 - 94 0 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgecuonuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgecuonuf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 97 | 98 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 97 98 - 94 0 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 97 98 - 94 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjyi9jm4l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjyi9jm4l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 6 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 260 - 2 5 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5hj3_hvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hj3_hvm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 6 chr1 3 260 - 2 0 chr1 65537 65544 - 65274 1 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 65537 65544 - 65274 3 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpujvngp00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujvngp00/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 6 chr1 3 260 - 2 0 chr1 65537 65544 - 65274 1 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 65537 65544 - 65274 3 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6o8jmity/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6o8jmity/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 6 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 260 - 2 5 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkk4nya4l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkk4nya4l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 6 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 65537 65794 - 65274 3 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=4, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqasyyght/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqasyyght/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 6 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 0 chr1 65537 65544 - 65274 1 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjludgqq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjludgqq2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 df2 Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 Actual Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 Expected Chromosome Start End Strand Distance 0 chr1 1 258 + 65280 1 chr1 1 258 - 65280 2 chr1 3 260 - 65278 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg42n53ox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg42n53ox/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 6 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 65537 | 65544 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 0 chr1 65537 65544 - 65274 1 chr1 65537 65544 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 3 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 65537 65544 - 65274 5 chr1 65537 65544 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 65537 65544 - 65274 4 chr1 65537 65544 - 65530 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmmh3payb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmh3payb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5vy5jfgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vy5jfgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 4 - 4 2 chr1 65537 65540 - 65274 3 chr1 65537 65540 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65274 9 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 6 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 1 4 - 4 2 chr1 65537 65540 - 65274 3 chr1 65537 65540 - 65530 4 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65274 8 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 9 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphm19fjg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphm19fjg1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 7 chr1 65537 65538 - 65274 8 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 7 chr1 65537 65538 - 65274 8 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_qx5l13z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_qx5l13z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps6mrxj9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6mrxj9i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqax9z7lj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqax9z7lj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaz4skdux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaz4skdux/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 6 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 6 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvixru43y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvixru43y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 6 chr1 65537 65538 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 df2 Chromosome Start End Strand Distance 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 6 chr1 65537 65538 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65534 1 chr1 65537 65538 - 65534 2 chr1 65537 65538 - 65534 3 chr1 65537 65538 - 65534 4 chr1 65537 65538 - 65534 5 chr1 65537 65538 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcwpqysnu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcwpqysnu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 8 chr1 65537 65538 - 65274 9 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 8 chr1 65537 65538 - 65274 9 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65274 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp33wmvhx7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33wmvhx7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 4 - 4 2 chr1 65537 65540 - 65274 3 chr1 65537 65540 - 65530 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 6 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65274 9 chr1 65537 65794 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65540 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 7 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65530 6 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 df2 Chromosome Start End Strand Distance 1 chr1 1 4 - 4 2 chr1 65537 65540 - 65274 3 chr1 65537 65540 - 65530 4 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65274 8 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 9 chr1 65537 65794 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 1 4 - 4 1 chr1 65537 65540 - 65274 2 chr1 65537 65540 - 65530 3 chr1 65537 65794 - 65274 4 chr1 65537 65794 - 65274 5 chr1 65537 65794 - 65274 6 chr1 65537 65794 - 65530 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7525auod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7525auod/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 0 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 1 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 + 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjebsoakf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjebsoakf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 1 chr1 1 258 - 65280 2 chr1 65537 65538 - 65530 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 258 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 258 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 2 chr1 1 258 - 65280 1 chr1 65537 65538 - 65530 df2 Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 1 chr1 1 258 - 65280 2 chr1 65537 65538 - 65530 Actual Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 1 chr1 1 258 - 65280 2 chr1 65537 65538 - 65530 Expected Chromosome Start End Strand Distance 0 chr1 1 258 - 65280 1 chr1 1 258 - 65280 2 chr1 65537 65538 - 65530 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp59lrvcp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59lrvcp3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_l8rtfss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_l8rtfss/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 6 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 6 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzvl5wd6m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzvl5wd6m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_oan8omu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_oan8omu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwjnpyrsh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwjnpyrsh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptj863v68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj863v68/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 2 2 chr1 3 6 - 2 0 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbgy0xqmh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgy0xqmh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 6 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 6 0 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 6 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyvrurw5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvrurw5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 6 chr1 65537 65538 - 65530 7 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 6 chr1 65537 65538 - 65530 7 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxrhbl6vt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrhbl6vt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 5 - 2 8 chr1 3 5 - 3 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 4 - 2 4 chr1 3 4 - 4 0 chr1 3 5 - 2 1 chr1 3 5 - 3 2 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 5 - 2 8 chr1 3 5 - 3 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1_kvkjv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1_kvkjv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 8 - 6 6 chr1 7 9 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7 | 9 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 8 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 7 8 - 6 0 chr1 7 9 - 6 1 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 df2 Chromosome Start End Strand Distance 5 chr1 7 8 - 6 6 chr1 7 9 - 6 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 Actual Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 Expected Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_onf1khi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_onf1khi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpssnofkm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssnofkm_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0kfvrjb1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kfvrjb1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 7 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 6 0 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 7 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnasov08e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnasov08e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 7 chr1 65537 65538 - 65530 8 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 7 chr1 65537 65538 - 65530 8 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn1wxg241/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn1wxg241/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 8 - 6 7 chr1 7 9 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 9 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 8 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 7 8 - 6 1 chr1 7 9 - 6 0 chr1 7 264 - 6 2 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 df2 Chromosome Start End Strand Distance 6 chr1 7 8 - 6 7 chr1 7 9 - 6 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 Actual Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 Expected Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1_q1z8m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1_q1z8m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 7 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 6 0 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 7 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxn1movev/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxn1movev/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf37an2hk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf37an2hk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyvqpl_i9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvqpl_i9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcgeu_dkz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgeu_dkz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_a7h08w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_a7h08w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfkxhh3wr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkxhh3wr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplg5ed1zg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplg5ed1zg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpop8l8h6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpop8l8h6r/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaqk8xsp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaqk8xsp3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 10 - 2 0 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_aj90xxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_aj90xxr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp36c72hb7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36c72hb7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_iyvavfn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_iyvavfn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpasr_7fio/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasr_7fio/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 4 - 2 8 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 3 4 - 2 4 chr1 3 4 - 4 1 chr1 3 10 - 2 0 chr1 3 260 - 2 2 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 4 - 2 8 chr1 3 4 - 4 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpimkqjxym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpimkqjxym/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 4 - 2 7 chr1 3 4 - 4 8 chr1 3 5 - 2 9 chr1 3 5 - 3 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 3 4 - 2 5 chr1 3 4 - 4 1 chr1 3 5 - 2 2 chr1 3 5 - 3 0 chr1 3 260 - 2 3 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 6 chr1 3 4 - 2 7 chr1 3 4 - 4 8 chr1 3 5 - 2 9 chr1 3 5 - 3 0 chr1 3 260 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp630o6lfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp630o6lfc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 8 - 6 7 chr1 7 9 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 9 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 8 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | | chr1 | 7 | 264 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 7 8 - 6 1 chr1 7 9 - 6 0 chr1 7 264 - 6 2 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 df2 Chromosome Start End Strand Distance 6 chr1 7 8 - 6 7 chr1 7 9 - 6 0 chr1 7 264 - 6 1 chr1 7 264 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 Actual Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 Expected Chromosome Start End Strand Distance 0 chr1 7 8 - 6 1 chr1 7 9 - 6 2 chr1 7 264 - 6 3 chr1 7 264 - 6 4 chr1 7 264 - 6 5 chr1 7 264 - 6 6 chr1 7 264 - 6 7 chr1 7 264 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4zm3l2vi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zm3l2vi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 df2 Chromosome Start End Strand Distance 7 chr1 65537 65794 - 65530 8 chr1 65537 65794 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclwrpk4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclwrpk4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2odrtmsb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2odrtmsb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp_7gbtof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_7gbtof/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplbg2dakd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbg2dakd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcyknv7c_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcyknv7c_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2yrmhct5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2yrmhct5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpas1wqocw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas1wqocw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqgtok5do/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqgtok5do/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxybswc06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxybswc06/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2up0e4r7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2up0e4r7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp72cjzuwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72cjzuwy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 10 - 65528 2 chr1 3 260 - 2 3 chr1 3 260 - 65278 4 chr1 3 260 - 2 5 chr1 3 260 - 65278 6 chr1 3 260 - 2 7 chr1 3 260 - 65278 8 chr1 3 260 - 2 9 chr1 3 260 - 65278 10 chr1 3 260 - 2 11 chr1 3 260 - 65278 12 chr1 3 260 - 2 13 chr1 3 260 - 65278 14 chr1 3 6 - 2 15 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 3 6 - 2 5 chr1 3 6 - 65532 2 chr1 3 10 - 2 3 chr1 3 10 - 65528 0 chr1 3 260 - 2 6 chr1 3 260 - 2 8 chr1 3 260 - 2 10 chr1 3 260 - 2 12 chr1 3 260 - 2 14 chr1 3 260 - 2 1 chr1 3 260 - 65278 7 chr1 3 260 - 65278 9 chr1 3 260 - 65278 11 chr1 3 260 - 65278 13 chr1 3 260 - 65278 15 chr1 3 260 - 65278 df2 Chromosome Start End Strand Distance 14 chr1 3 6 - 2 15 chr1 3 6 - 65532 0 chr1 3 10 - 2 1 chr1 3 10 - 65528 2 chr1 3 260 - 2 4 chr1 3 260 - 2 6 chr1 3 260 - 2 8 chr1 3 260 - 2 10 chr1 3 260 - 2 12 chr1 3 260 - 2 3 chr1 3 260 - 65278 5 chr1 3 260 - 65278 7 chr1 3 260 - 65278 9 chr1 3 260 - 65278 11 chr1 3 260 - 65278 13 chr1 3 260 - 65278 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 65532 2 chr1 3 10 - 2 3 chr1 3 10 - 65528 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 10 chr1 3 260 - 65278 11 chr1 3 260 - 65278 12 chr1 3 260 - 65278 13 chr1 3 260 - 65278 14 chr1 3 260 - 65278 15 chr1 3 260 - 65278 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 65532 2 chr1 3 10 - 2 3 chr1 3 10 - 65528 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 9 chr1 3 260 - 2 10 chr1 3 260 - 65278 11 chr1 3 260 - 65278 12 chr1 3 260 - 65278 13 chr1 3 260 - 65278 14 chr1 3 260 - 65278 15 chr1 3 260 - 65278 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc4khfd27/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc4khfd27/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjybqxbdj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjybqxbdj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvw0lzw4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvw0lzw4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcwo5h8ks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcwo5h8ks/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 8 chr1 65537 65794 - 65530 9 chr1 65537 65794 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65794 | a | 0 | ... | | chr1 | 65537 | 65794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 df2 Chromosome Start End Strand Distance 8 chr1 65537 65794 - 65530 9 chr1 65537 65794 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65794 - 65530 1 chr1 65537 65794 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo1ikt_1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1ikt_1d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 4 - 2 12 chr1 3 4 - 4 13 chr1 3 4 - 2 14 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 13 chr1 3 4 - 2 1 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 14 chr1 3 4 - 4 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 13 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 14 chr1 3 4 - 4 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 2 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 4 - 4 13 chr1 3 4 - 4 14 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 2 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 4 - 4 13 chr1 3 4 - 4 14 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=15, step=1) index equal [ True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnfm9oh9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnfm9oh9u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 6 - 2 3 chr1 3 6 - 2 1 chr1 3 10 - 2 0 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 7 chr1 3 6 - 2 0 chr1 3 10 - 2 1 chr1 3 260 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 6 - 2 2 chr1 3 10 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 8 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 2 1 chr1 3 10 - 2 2 chr1 3 260 - 2 3 chr1 3 260 - 2 4 chr1 3 260 - 2 5 chr1 3 260 - 2 6 chr1 3 260 - 2 7 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq95bqopa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq95bqopa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 4 - 2 12 chr1 3 4 - 4 13 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 13 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 14 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 13 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 6 - 2 13 chr1 3 6 - 2 14 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 6 - 2 13 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=14, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2f7n6pc5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f7n6pc5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 4 - 2 12 chr1 3 4 - 4 13 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 13 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 14 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 13 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 6 - 2 13 chr1 3 6 - 2 14 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 4 - 4 12 chr1 3 6 - 2 13 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=14, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpox7mzbkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpox7mzbkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_0vv_tay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_0vv_tay/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgikd0nuc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgikd0nuc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 3 chr1 1 2 - 65536 4 chr1 1 2 - 65536 5 chr1 1 2 - 65536 6 chr1 1 2 - 65536 7 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ocvue02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ocvue02/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclqa17zr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclqa17zr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 6 - 2 11 chr1 3 6 - 2 12 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 6 - 2 11 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=12, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd10ia4a7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd10ia4a7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 4 - 2 10 chr1 3 4 - 4 11 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 11 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 12 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 11 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 6 - 2 11 chr1 3 6 - 2 12 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 2 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 4 - 4 10 chr1 3 6 - 2 11 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=12, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpasu3vwt3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpasu3vwt3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 4 - 2 8 chr1 3 4 - 4 9 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 9 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 10 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 9 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 6 - 2 9 chr1 3 6 - 2 10 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 4 - 4 8 chr1 3 6 - 2 9 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=10, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq9yarz9g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9yarz9g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 4 - 2 6 chr1 3 4 - 4 7 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 7 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 8 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 5 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 6 chr1 3 4 - 4 7 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 6 chr1 3 6 - 2 7 chr1 3 6 - 2 8 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 6 chr1 3 6 - 2 7 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=8, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm_fq4_0w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_fq4_0w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 5 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 5 chr1 3 4 - 2 1 chr1 3 4 - 4 6 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 6 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=6, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcz76jebg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcz76jebg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 6 - 2 3 chr1 3 6 - 2 4 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 6 - 2 3 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=4, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp01lzbr8s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01lzbr8s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 + 65528 1 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppqt556cz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppqt556cz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 + 65528 1 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfrns4dy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfrns4dy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 65534 1 chr1 3 4 - 65534 2 chr1 3 4 - 65534 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptbzuc4st/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbzuc4st/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 65536 1 chr1 1 2 - 65536 2 chr1 1 2 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3z_nnmdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3z_nnmdq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 65537 65538 - 65530 1 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd3u9aaw4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3u9aaw4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9wxnn9px/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9wxnn9px/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 3 chr1 1 2 - 6 1 chr1 65537 65538 - 65530 2 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfgc8ofv9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgc8ofv9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmsaqz9ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsaqz9ig/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 3 chr1 65537 65538 - 65530 4 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 3 chr1 1 2 - 6 4 chr1 1 2 - 6 1 chr1 65537 65538 - 65530 2 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 3 chr1 65537 65538 - 65530 4 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 3 chr1 65537 65538 - 65530 4 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 2 - 6 3 chr1 65537 65538 - 65530 4 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoysf88io/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoysf88io/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 3 chr1 1 2 - 6 1 chr1 65537 65538 - 65530 2 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3ineciq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3ineciq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 65537 | 65538 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 3 chr1 1 2 - 6 1 chr1 65537 65538 - 65530 2 chr1 65537 65538 - 65536 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 65537 65538 - 65530 3 chr1 65537 65538 - 65536 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj100fec8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj100fec8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 + 65528 1 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38aw2mi2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38aw2mi2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 + 65528 1 chr1 3 6 - 65532 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 df2 Chromosome Start End Strand Distance 1 chr1 3 6 - 65532 0 chr1 3 10 + 65528 Actual Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Expected Chromosome Start End Strand Distance 0 chr1 3 6 - 65532 1 chr1 3 10 + 65528 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptj5sk76e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj5sk76e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 3 chr1 3 4 - 2 1 chr1 3 4 - 4 4 chr1 3 4 - 4 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9jq4dl07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jq4dl07/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 260 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 260 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 3 chr1 3 4 - 2 1 chr1 3 4 - 4 4 chr1 3 4 - 4 2 chr1 3 260 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 0 chr1 3 260 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 260 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 260 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpehqdwh78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpehqdwh78/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 6 - 2 4 chr1 3 6 - 2 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 6 - 2 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 6 - 2 3 chr1 3 6 - 2 4 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 6 - 2 3 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=4, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0m40ro6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0m40ro6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 10 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 2 4 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 10 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 3 chr1 3 4 - 2 1 chr1 3 4 - 4 4 chr1 3 4 - 4 2 chr1 3 10 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 3 chr1 3 4 - 2 2 chr1 3 4 - 4 4 chr1 3 4 - 4 0 chr1 3 10 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 10 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 10 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2qncc8_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2qncc8_v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhq5w64v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhq5w64v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 2 chr1 1 2 - 6 1 chr1 1 3 - 5 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpavwsvtq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavwsvtq5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 5 chr1 3 4 - 4 2 chr1 3 5 - 2 3 chr1 3 5 - 3 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbv83ps7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbv83ps7q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfhjcdkht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfhjcdkht/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 2 chr1 1 2 - 6 1 chr1 1 3 - 5 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjqd7ezvj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqd7ezvj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 2 chr1 1 2 - 6 1 chr1 1 3 - 5 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 1 2 - 6 2 chr1 1 3 - 5 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoxtr4b8i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxtr4b8i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 6 0 chr1 3 4 - 2 1 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa48psvy1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa48psvy1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 6 0 chr1 3 4 - 2 1 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc2a_7mb8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2a_7mb8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 6 0 chr1 3 4 - 2 1 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf2dzugyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2dzugyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcl6nnglh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcl6nnglh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2yxcb_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2yxcb_7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8cg8nqyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8cg8nqyj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 2 5 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnqpa9oz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnqpa9oz2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gvsk0qj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gvsk0qj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6kpf2op6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6kpf2op6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 2 5 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz23uovjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz23uovjj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 5 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3 4 - 2 4 chr1 3 4 - 2 3 chr1 3 4 - 4 5 chr1 3 4 - 4 0 chr1 3 5 - 2 1 chr1 3 5 - 3 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 5 - 2 5 chr1 3 5 - 3 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps7_wyw2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps7_wyw2b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmf2whqfz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmf2whqfz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 6 0 chr1 3 4 - 2 1 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 6 1 chr1 3 4 - 2 2 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkyzx22ww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyzx22ww/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 - 4 df2 Chromosome Start End Strand Distance 0 chr2 1 2 - 4 Actual Chromosome Start End Strand Distance 0 chr2 1 2 - 4 Expected Chromosome Start End Strand Distance 0 chr2 1 2 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsai1nl_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsai1nl_t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm3hckwxt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3hckwxt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_4jkwrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_4jkwrw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr1v01et6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr1v01et6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprvl50v7o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprvl50v7o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 2 5 chr1 3 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 4 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 4 - 4 5 chr1 3 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaipgmjbk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaipgmjbk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 4 - 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 4 - 4 df2 Chromosome Start End Strand Distance 0 chr2 1 4 - 4 Actual Chromosome Start End Strand Distance 0 chr2 1 4 - 4 Expected Chromosome Start End Strand Distance 0 chr2 1 4 - 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa25fs_fe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa25fs_fe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf19rjv5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf19rjv5i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2hw0qp0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hw0qp0e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr9jvda47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr9jvda47/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0wrpgus3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0wrpgus3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3ahn1nod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ahn1nod/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ok96lkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ok96lkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 4 2 chr1 3 4 - 2 3 chr1 3 4 - 4 4 chr1 3 6 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | | chr1 | 3 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 df2 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 2 chr1 3 4 - 2 1 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 5 chr1 3 6 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 1 chr1 3 4 - 2 2 chr1 3 4 - 4 3 chr1 3 4 - 4 4 chr1 3 6 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. =============================== warnings summary =============================== tests/conftest.py:83 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/conftest.py:83: SyntaxWarning: invalid escape sequence '\s' sep="\s+", pyranges/__init__.py:18: 13 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/__init__.py:18: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources tests/test_binary.py:118: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:118: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:139: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:139: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:160: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:160: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:187: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:187: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:212: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:212: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:291: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:291: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:329: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:329: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:368: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:368: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:392: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:392: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:426: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:426: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:516: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:516: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:579: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:579: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) pyranges/methods/init.py:60: 60 warnings .pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py: 9 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 161834 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 159199 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_getset_attr.py: 3 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_io.py: 4 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_pickle.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 6 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 358 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 25984 warnings .pybuild/cpython3_3.12_pyranges/build/tests/windows/test_windows.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 8 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_count_overlaps.py: 1 warning /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:60: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. return {k: v for k, v in df.groupby(grpby_key)} pyranges/methods/init.py:189: 48 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 4556 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 2000 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 6773 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 7 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:189: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby("Chromosome") tests/test_do_not_error.py:46: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py:46: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:35: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:35: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:100: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:100: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:163: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:163: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:205: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:205: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:234: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:234: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:272: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:272: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:287: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:287: HypothesisDeprecationWarning: The return_value health check is deprecated, because this is always an error. @settings( tests/test_unary.py:315: 12 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:315: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 8380 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 16531 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 17602 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/tostring2.py:31: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. df = pd.concat([plus, minus]) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 1368 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:3779: FutureWarning: The behavior of Series.replace (and DataFrame.replace) with CategoricalDtype is deprecated. In a future version, replace will only be used for cases that preserve the categories. To change the categories, use ser.cat.rename_categories instead. other.Strand = other.Strand.replace({"+": "-", "-": "+"}) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 3239 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 119 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 5773 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 1 warning /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:187: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby(["Chromosome", "Strand"]) .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1217804. 1221351. 1223357. 1223968. 1227319. 1228946. 1232031.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1336515. 1337055. 1338183. 1338436. 1338653. 1339812. 1340190. 1340365. 1340503. 1342156. 1342484. 1342758. 1349350.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1311924. 1312147. 1313592. 1315697. 1317450. 1321096. 1321984. 1323287. 1324691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1293708. 1293933. 1294199. 1294628. 1295008. 1295554. 1295938. 1296109. 1296280. 1296633. 1297933. 1298265. 1298421. 1299905. 1300068. 1300202. 1300692. 1302046. 1302975. 1305929. 1307156. 1307383. 1308018. 1309609.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1084506. 1085310. 1086012. 1087636. 1092294. 1092813. 1106127. 1106871. 1115075. 1116361.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1472089. 1477350. 1478745. 1479108. 1480936. 1482303. 1482662. 1485171. 1486235. 1486668. 1487914. 1490671. 1497848.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1255487. 1256335. 1257130. 1257310. 1262390. 1263569. 1264830. 1266290. 1267992. 1271637. 1273885.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1173926. 1174321. 1174489. 1175034. 1179333. 1179853. 1180340. 1180884. 1181815. 1182446. 1183047. 1184091. 1185864. 1196488. 1196716. 1197186. 1197935.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1281610. 1282010. 1282319. 1284090. 1285664. 1286278. 1286975. 1287299. 1287836. 1288037. 1290388. 1290555. 1290694. 1290953. 1291140. 1292029.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1353946. 1354106. 1354509. 1355752. 1356704. 1358794. 1361777.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1331536. 1331938. 1332806. 1333124. 1333379. 1335306.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1308720. 1308972. 1309851. 1311071. 1311677.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000169972.11' 'ENSG00000169972.11' 'ENSG00000169972.11' 'ENSG00000169972.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1373902. 1375495.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000175756.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1235041.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 818202. 819837.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000177757.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1435146. 1435821. 1437484. 1442882.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000179403.11' 'ENSG00000179403.11' 'ENSG00000179403.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1242646. 1243552. 1244275. 1244724. 1246722.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000184163.3' 'ENSG00000184163.3' 'ENSG00000184163.3' 'ENSG00000184163.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 65433. 65573. 71585.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186092.6' 'ENSG00000186092.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1211832. 1212138. 1212704. 1213785. 1214138.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186827.10' 'ENSG00000186827.10' 'ENSG00000186827.10' 'ENSG00000186827.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1203968. 1204236. 1204486. 1205680. 1206691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186891.13' 'ENSG00000186891.13' 'ENSG00000186891.13' 'ENSG00000186891.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 966614. 966803. 970423. 970601. 971006. 971208. 971523. 972150. 972424. 973010. 973326. 973640. 974051. 974364. 975108. 975865.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1001281. 1008279. 1013576. 1014540.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187608.9' 'ENSG00000187608.9' 'ENSG00000187608.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 924948. 925189. 925800. 926013. 930336. 931089. 935896. 939129. 939460. 940462. 941306. 943058. 943377. 944581.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 976269. 976641. 981029. 981173. 982093.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187642.9' 'ENSG00000187642.9' 'ENSG00000187642.9' 'ENSG00000187642.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 960800. 961750. 962478. 962917. 963253. 963504. 964008. 964180. 964530. 965715.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1020373. 1022462. 1034703. 1035324. 1040880. 1041397. 1041702. 1042162. 1043457. 1043732. 1044023. 1044257. 1044439. 1045277. 1045523. 1045876. 1046088. 1046349. 1046735. 1046957. 1047454. 1047687. 1047895. 1048365. 1049059. 1049451. 1049795. 1050037. 1050329. 1050591. 1050837. 1051043. 1051369. 1051645. 1051815. 1053977. 1054551. 1056118.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 999432. 1000172.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188290.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 944800. 945146. 945422. 945653. 946286. 947060. 948232. 948603. 951238. 952139. 952600. 953288. 953892. 954523. 956013. 956215. 957025. 959081. 959309.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1512473. 1516088. 1517412. 1517775. 1518990. 1520306. 1520617.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 634922.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1169087.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1426385. 1427787.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000205116.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1176396. 1179555.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000205231.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1167952.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1167198.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1450758. 1452122. 1452434. 1454500. 1455519. 1455916. 1456349. 1457180. 1459231. 1460917. 1462708. 1470158.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1059846. 1060393. 1061117. 1063201. 1063566. 1064401. 1064589. 1065475. 1066456. 1066667. 1067646. 1068003. 1068724. 1069355.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1387582. 1387869. 1388743. 1388830. 1389047. 1389473. 1390371. 1390563. 1392803. 1393460. 1395537. 1398366. 1398956. 1399328.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 157887.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 758336.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1379032.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 921016.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1137110. 1141032. 1144056.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000223823.1' 'ENSG00000223823.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 12227. 12721. 13052. 14409.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000223972.5' 'ENSG00000223972.5' 'ENSG00000223972.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1325102. 1325595. 1327032. 1328897.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000224051.6' 'ENSG00000224051.6' 'ENSG00000224051.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1402046.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1012190. 1013193.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000224969.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1430954. 1431843. 1434573.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000225285.1' 'ENSG00000225285.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 630683.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 827522.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1420564. 1422691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000225905.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 629433.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 14501. 15038. 15947. 16765. 17055. 17368. 17742. 18061. 18366. 24891. 29570.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 729804. 733364. 735613. 743350. 744391. 744825. 746818. 756141. 759123. 765247. 766387. 768613. 769712. 773107. 774280. 778626.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 259025. 261634. 268204. 268816. 289370. 297502. 357586. 358183. 359681.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 825552. 826923. 827775. 827853. 829104. 831677. 842020. 847806. 849602. 850351. 852515. 852766. 859446.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 633438.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 724360. 724903.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000229376.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 761154. 761989.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000229905.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 586358. 586955. 588453. 594756. 598551. 601577. 608056. 612864. 627823. 628223. 629006. 631204. 633129. 698959. 702340. 703789. 711922. 720206. 724564. 732212. 733064. 827796.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 801163. 805891. 808623. 810170. 817712.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230092.7' 'ENSG00000230092.7' 'ENSG00000230092.7' 'ENSG00000230092.7']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 868675. 869575. 870201. 875155. 876903.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230368.2' 'ENSG00000230368.2' 'ENSG00000230368.2' 'ENSG00000230368.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1275299. 1279393. 1280420.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230415.1' 'ENSG00000230415.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 911473. 914948.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230699.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1008229.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 489387. 489906.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000233653.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 134836.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 874349.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1419549. 1420592. 1421769.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000235098.8' 'ENSG00000235098.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 587729. 594768.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000235146.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 358957. 360168. 366052.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000236601.2' 'ENSG00000236601.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 348366.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 365692. 366151. 368450. 373323. 379972. 476945. 485208. 489553. 494898. 495049. 495476. 496605. 497299. 498305. 499369. 501620. 502243. 502955. 505103. 514423. 517266. 522928.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1072575. 1074307.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237330.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 779092. 782191. 783363. 784977. 787672. 793041. 795582. 801876. 803667. 804222. 805270. 806459. 807465. 810060.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 35174. 35481. 36081.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237613.2' 'ENSG00000237613.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 632616.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 91629. 92240. 111357. 112804. 120932. 129223. 133723.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 139847. 140339.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000239906.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 90050. 91105.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000239945.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 57653. 58856. 64116.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000240361.2' 'ENSG00000240361.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 633741.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1317899. 1318689.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000240731.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 914444. 914971.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241180.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 160690. 161525.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241599.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 143011. 149707. 155831. 164791. 165942. 168165. 168767. 169264. 172688. 173862.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1402601. 1407019. 1407313.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000242485.5' 'ENSG00000242485.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1055215. 1056116.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000242590.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 30039. 30667. 31109.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000243485.5' 'ENSG00000243485.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 634376.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 491989. 493241.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000250575.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1251334.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1405752.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 53312.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 675265.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 135895.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 440232.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 137965.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1170343.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 904957. 915976.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000272438.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1410618.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 998051.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1062808. 1063288.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000273443.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 187958.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1296170.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 17436.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 516479.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 632413.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 185350. 185559. 186469. 187287. 187577. 187890. 188266. 188584. 188902. 195411.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 182746. 183216. 183571. 183901. 184174.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000279928.2' 'ENSG00000279928.2' 'ENSG00000279928.2' 'ENSG00000279928.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 874591. 875155. 875625. 876611. 877234.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000283040.1' 'ENSG00000283040.1' 'ENSG00000283040.1' 'ENSG00000283040.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1312566.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 30503.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1339708.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 686673.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 451697.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1503661. 1509452.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000284740.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 782050.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1098113. 1104598.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000285812.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:153: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. result_df.Cluster.replace(cluster_ids, inplace=True) .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for _, gdf in natsorted(df.groupby(groupby)): .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['+', '+', '-', NaN, NaN] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[NaN, NaN, NaN, '+', '-'] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] - ValueErr... ========= 1 failed, 530 passed, 418337 warnings in 4128.40s (1:08:48) ========== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 12 dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13 make: *** [debian/rules:22: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1596758 and its subdirectories pyranges failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/pyranges_0.0.111+ds-8.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/pyranges_0.0.111+ds-8.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/pyranges_0.0.111+ds-8.build1.log.gz' Fri Sep 27 02:47:17 UTC 2024 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 95.5% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-27 02:47:18] INFO: Starting at 2024-09-27 02:47:18.117565 [2024-09-27 02:47:18] INFO: Generating the pages of 1 package(s) [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/pyranges_0.0.111+ds-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/pyranges_0.0.111+ds-8.diff.gz is missing [2024-09-27 02:47:18] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/armhf/pyranges_0.0.111+ds-7_armhf.buildinfo [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/pyranges_0.0.111+ds-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/pyranges_0.0.111+ds-7.diff.gz is missing [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/pyranges_0.0.111+ds-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/pyranges_0.0.111+ds-8.diff.gz is missing [2024-09-27 02:47:18] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/pyranges didn't produce a buildlog, even though it has been built. [2024-09-27 02:47:18] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/armhf/pyranges_0.0.111+ds-7_armhf.buildinfo [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/pyranges_0.0.111+ds-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/pyranges_0.0.111+ds-7.diff.gz is missing [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/pyranges_0.0.111+ds-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/pyranges_0.0.111+ds-7.diff.gz is missing [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/pyranges_0.0.111+ds-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/pyranges_0.0.111+ds-4.diff.gz is missing [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/pyranges_0.0.111+ds-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/pyranges_0.0.111+ds-4.diff.gz is missing [2024-09-27 02:47:18] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/bullseye/armhf/pyranges_0.0.85+ds-1_armhf.buildinfo [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/pyranges_0.0.85+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/pyranges_0.0.85+ds-1.diff.gz is missing [2024-09-27 02:47:18] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/pyranges_0.0.85+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/pyranges_0.0.85+ds-1.diff.gz is missing [2024-09-27 02:47:18] INFO: Finished at 2024-09-27 02:47:18.528206, took: 0:00:00.410646 Fri Sep 27 02:47:18 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/pyranges.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/pyranges_0.0.111+ds-8.rbuild.log: 95.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/pyranges_0.0.111+ds-8.rbuild.log.gz [2024-09-27 02:47:19] INFO: Starting at 2024-09-27 02:47:19.096195 [2024-09-27 02:47:19] INFO: Generating the pages of 1 package(s) [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/pyranges_0.0.111+ds-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/pyranges_0.0.111+ds-8.diff.gz is missing [2024-09-27 02:47:19] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/armhf/pyranges_0.0.111+ds-7_armhf.buildinfo [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/pyranges_0.0.111+ds-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/pyranges_0.0.111+ds-7.diff.gz is missing [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/pyranges_0.0.111+ds-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/pyranges_0.0.111+ds-8.diff.gz is missing [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/pyranges_0.0.111+ds-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/pyranges_0.0.111+ds-8.diff.gz is missing [2024-09-27 02:47:19] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/armhf/pyranges_0.0.111+ds-7_armhf.buildinfo [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/pyranges_0.0.111+ds-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/pyranges_0.0.111+ds-7.diff.gz is missing [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/pyranges_0.0.111+ds-7.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/pyranges_0.0.111+ds-7.diff.gz is missing [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/pyranges_0.0.111+ds-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/pyranges_0.0.111+ds-4.diff.gz is missing [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/pyranges_0.0.111+ds-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/pyranges_0.0.111+ds-4.diff.gz is missing [2024-09-27 02:47:19] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/bullseye/armhf/pyranges_0.0.85+ds-1_armhf.buildinfo [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/pyranges_0.0.85+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/pyranges_0.0.85+ds-1.diff.gz is missing [2024-09-27 02:47:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/pyranges_0.0.85+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/pyranges_0.0.85+ds-1.diff.gz is missing [2024-09-27 02:47:19] INFO: Finished at 2024-09-27 02:47:19.498314, took: 0:00:00.402124 All cleanup done. Fri Sep 27 02:47:19 UTC 2024 - total duration: 1h 10m 30s. Fri Sep 27 02:47:19 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-cFvSFGEb, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1h 10min 32.589s CPU time consumed: 6.417s