2024-10-17T05:37:07,146 Disabling truststore because Python version isn't 3.10+ 2024-10-17T05:37:07,631 Created temporary directory: /tmp/pip-build-tracker-23c3sqk5 2024-10-17T05:37:07,632 Initialized build tracking at /tmp/pip-build-tracker-23c3sqk5 2024-10-17T05:37:07,632 Created build tracker: /tmp/pip-build-tracker-23c3sqk5 2024-10-17T05:37:07,632 Entered build tracker: /tmp/pip-build-tracker-23c3sqk5 2024-10-17T05:37:07,633 Created temporary directory: /tmp/pip-wheel-l06dwouk 2024-10-17T05:37:07,638 Created temporary directory: /tmp/pip-ephem-wheel-cache-jawrqmu4 2024-10-17T05:37:07,682 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-10-17T05:37:07,685 2 location(s) to search for versions of biocode: 2024-10-17T05:37:07,685 * https://pypi.org/simple/biocode/ 2024-10-17T05:37:07,685 * https://www.piwheels.org/simple/biocode/ 2024-10-17T05:37:07,685 Fetching project page and analyzing links: https://pypi.org/simple/biocode/ 2024-10-17T05:37:07,686 Getting page https://pypi.org/simple/biocode/ 2024-10-17T05:37:07,687 Found index url https://pypi.org/simple/ 2024-10-17T05:37:07,708 Fetched page https://pypi.org/simple/biocode/ as application/vnd.pypi.simple.v1+json 2024-10-17T05:37:07,713 Found link https://files.pythonhosted.org/packages/e1/6d/8b417c8c08f02c960801f360bc8b38927a4c14dfee8cb1418978bdfc4946/biocode-0.1.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.0 2024-10-17T05:37:07,714 Found link https://files.pythonhosted.org/packages/96/e5/314879e7d54bee7e0ed6db1fc358d193ae2d118e4825a99d14f3269a9322/biocode-0.1.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.1 2024-10-17T05:37:07,714 Found link https://files.pythonhosted.org/packages/4e/94/c999970e61e13f3082eae7989bc32d745ef7d846824252dd9a3c09cfd19c/biocode-0.1.2.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.2 2024-10-17T05:37:07,714 Found link https://files.pythonhosted.org/packages/a5/2c/85a52abaf0192795d5fbc56842c58c349bc6b58c568b4b913b8fdf591617/biocode-0.1.3.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.3 2024-10-17T05:37:07,715 Found link https://files.pythonhosted.org/packages/a5/06/562772ff9d04bcfcde87ed1ce76026eaf8f6b15cf7336fc6334bad04db00/biocode-0.1.4.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.4 2024-10-17T05:37:07,715 Found link https://files.pythonhosted.org/packages/27/c6/cdb7baa2821259f68c059a9e7385d613b817d90c00c8e727df7d3da23d2e/biocode-0.1.5.tar.gz (from https://pypi.org/simple/biocode/), version: 0.1.5 2024-10-17T05:37:07,715 Found link https://files.pythonhosted.org/packages/5d/ff/bda52fd80d3696809f96b27e1df816809c610a91587199fbb5611a82ff48/biocode-0.2.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.2.0 2024-10-17T05:37:07,715 Found link https://files.pythonhosted.org/packages/4b/d4/61d22deda78a8fb9b998ac1a7e7fee95eb3e84adcb26ab1705fda8235d31/biocode-0.3.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.3.0 2024-10-17T05:37:07,716 Found link https://files.pythonhosted.org/packages/9e/04/4a879cb84c7d4d8a11b9812e25668e5f1d4ef5e3cea429f7cc8202a0021b/biocode-0.3.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.3.1 2024-10-17T05:37:07,716 Found link https://files.pythonhosted.org/packages/72/af/9de76d7a8ae1cc6912488e33e53df8145aac259d36ddd42fc3dc803ea473/biocode-0.4.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.0 2024-10-17T05:37:07,716 Found link https://files.pythonhosted.org/packages/c7/93/31d3a353be167da9500e2bdff93451dba1a6a134e425767d426e297a0853/biocode-0.4.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.1 2024-10-17T05:37:07,717 Found link https://files.pythonhosted.org/packages/7a/24/cae23280630c49008e96590c77494485e47bbcf488f5c4b4e03ecc7b1e29/biocode-0.4.2.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.2 2024-10-17T05:37:07,717 Found link https://files.pythonhosted.org/packages/7f/5a/0d11038818cc78cee863d20da8a16a9907c20be8bfa8334ebabec4cb37e4/biocode-0.4.4.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.4 2024-10-17T05:37:07,717 Found link https://files.pythonhosted.org/packages/43/8e/107a8d911b7af9db94a561f6740801f62b69a60cb8857fc6642268f0d99d/biocode-0.4.5.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.5 2024-10-17T05:37:07,717 Found link https://files.pythonhosted.org/packages/02/e7/dc62a42fcfcb2288f397789f6bc83fd40a815d495edba4fa79e14759935c/biocode-0.4.7.tar.gz (from https://pypi.org/simple/biocode/), version: 0.4.7 2024-10-17T05:37:07,718 Found link https://files.pythonhosted.org/packages/f2/fc/483f6dad337423c04dc8a1b2756c3e5326e9381648e5560eb602a4f83413/biocode-0.5.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.5.0 2024-10-17T05:37:07,718 Found link https://files.pythonhosted.org/packages/5c/b7/035e01334320dd66ac8c65be4baa910e8cb16215c563d7b65bfdfd5b56d6/biocode-0.5.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.5.1 2024-10-17T05:37:07,718 Found link https://files.pythonhosted.org/packages/95/f7/e7ac262a9e90ac52d889c0a832aa8276b95fb6c23d0c65bf32fc2ccc1c7a/biocode-0.5.2.tar.gz (from https://pypi.org/simple/biocode/), version: 0.5.2 2024-10-17T05:37:07,718 Found link https://files.pythonhosted.org/packages/3b/2d/43287226a16b06ecdf7ed706752de718042382513bf2a3a5b0c9d2a41222/biocode-0.5.3.tar.gz (from https://pypi.org/simple/biocode/), version: 0.5.3 2024-10-17T05:37:07,719 Found link https://files.pythonhosted.org/packages/b3/e7/e8b3bd627d57954933c9c5a79bbdf28ad93073cc0792c61f71e3777f44d8/biocode-0.6.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.6.0 2024-10-17T05:37:07,719 Found link https://files.pythonhosted.org/packages/dd/d7/73e00082816c193207ea58420b38ac0a4041d345b8617f0d15501367c080/biocode-0.7.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.7.0 2024-10-17T05:37:07,719 Found link https://files.pythonhosted.org/packages/bb/7a/c073ca257a937286fec9e225190fa55c66a46132708e8dfa13569ef0cc37/biocode-0.7.1.tar.gz (from https://pypi.org/simple/biocode/), version: 0.7.1 2024-10-17T05:37:07,719 Found link https://files.pythonhosted.org/packages/a3/b5/0a5b44de28177113d5bbc0a8b510ea6e9acf82184b1e1ad5303357d1caa5/biocode-0.8.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.8.0 2024-10-17T05:37:07,720 Found link https://files.pythonhosted.org/packages/ac/58/b16f07e13b99403a0069b7782dc963882f634b6863d6e4bba85d327bd634/biocode-0.9.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.9.0 2024-10-17T05:37:07,720 Found link https://files.pythonhosted.org/packages/60/4d/1ede29387210a62ff0c6ccbb1c467e94890fb1a5802a2a3b3d37df3997cb/biocode-0.10.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.10.0 2024-10-17T05:37:07,720 Found link https://files.pythonhosted.org/packages/8e/56/e76dfd9f0785ac5a835f275a4b6b35cc4fff7c8195f85ade37fb76a133bd/biocode-0.11.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.11.0 2024-10-17T05:37:07,720 Found link https://files.pythonhosted.org/packages/76/b9/22a5ad1d471977fa223d22f5dfe57f099f1262fdd3fab678dfe555f11344/biocode-0.12.0.tar.gz (from https://pypi.org/simple/biocode/), version: 0.12.0 2024-10-17T05:37:07,721 Fetching project page and analyzing links: https://www.piwheels.org/simple/biocode/ 2024-10-17T05:37:07,721 Getting page https://www.piwheels.org/simple/biocode/ 2024-10-17T05:37:07,722 Found index url https://www.piwheels.org/simple/ 2024-10-17T05:37:07,761 Fetched page https://www.piwheels.org/simple/biocode/ as text/html 2024-10-17T05:37:07,768 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.11.0-py3-none-any.whl#sha256=12935f1029ccce1fa148acb48dcdd715b3ead3f188052f41158f6beb93820b96 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,769 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.10.0-py3-none-any.whl#sha256=176b55ba344b86385e86406fceaafb4dc19b817ed6ef96cc353386889ff6e709 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,769 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.9.0-py3-none-any.whl#sha256=501bd0384472d48e49c3ff2720c2ab87757414d567897589d38475113d0cdfff (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,769 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.8.0-py3-none-any.whl#sha256=e7072ae4de4a03bb9e9643e1161fcd0d8df3f543aab05b8b275799f5172f72b6 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,769 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.7.1-py3-none-any.whl#sha256=8a4879e5efc9060b185c19b016b32d855dcc3c5ced8cb614484771c21474ac71 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,770 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.7.0-py3-none-any.whl#sha256=7440f5b1d70473f68e2c42b99ce36bb23229dac2f5c1d59d287fe59f6b9fa8c6 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,770 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.6.0-py3-none-any.whl#sha256=f638223164aad0892b1f4e3ff59e5c70bf598b95f242467fc1aa28dc100436b6 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,770 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.5.3-py3-none-any.whl#sha256=d47b9988366ce2efc4b61fa29fa149d6518a5abd2b645ef30ca873b2a156d656 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,770 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.5.2-py3-none-any.whl#sha256=87ef8c0b656cb96cbddffb44f82a3f7d40334636f9919dd335b7aac6d872331e (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,770 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.5.1-py3-none-any.whl#sha256=bf9a0479e6b373349ff4d030deed21980a2b0adab49430c21616bd78cdf290b1 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,771 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.5.0-py3-none-any.whl#sha256=6ce7d47e815c46602fb4ba8a8764d62c5f26910a6c168c63956baf4983f90a45 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,771 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.7-py3-none-any.whl#sha256=c6f756e5d1f8d1c212a939c1081689f81a283788ef9a4b6c034eea0031d77ac3 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,771 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.5-py3-none-any.whl#sha256=932e531e5c3c1007b4b797e8f95973867123104ae76b7f79a2603520f2420370 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,771 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.4-py3-none-any.whl#sha256=b61ad63c7d700f55cd2db1a75a68d247d54f08fcd6ec9308b547a5f1ea0ce0fe (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,771 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.2-py3-none-any.whl#sha256=e3bae2595434c4a01ca3c8128147d556b5bde54d82faf923f41413864cea2b0d (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,771 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.1-py3-none-any.whl#sha256=521f2d73f74c744fbe98259bd0c5246da47360c2f15cc9673dd508810a483917 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,772 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.4.0-py3-none-any.whl#sha256=c0167fa70e63b6ae969ba2a625bde0f55968889d65db61a195bccb8c7a36301e (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,772 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.3.1-py3-none-any.whl#sha256=da177825df75c57e89f9af93b45c99d0d43e1bd1c9b98b20396d1f80ac764f09 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,772 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.3.0-py3-none-any.whl#sha256=db84b6266a91bbdab2b21a249781b03776481f1ba3521c28b2c5af244e40f6d5 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,772 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.2.0-py3-none-any.whl#sha256=552b663044ffd5a76d432ac46e0b3ed5d11cd065bb16cc3598b0bdb77595b7ff (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,772 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.1.5-py3-none-any.whl#sha256=d036768387d015aac47397bce617b23c510f102a026ef9c488626d9c0697694f (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,773 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.1.4-py3-none-any.whl#sha256=70e1a456c4373ebf44860b89f3555173e027e3c4f35c51d65c6101a574a1c8ef (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,773 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.1.3-py3-none-any.whl#sha256=550c92b8b5e8d214a4e6b7e0dfca8932059095749a2d7d77d326c867e6b19154 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,773 Skipping link: No binaries permitted for biocode: https://www.piwheels.org/simple/biocode/biocode-0.1.2-py3-none-any.whl#sha256=cccf2290fd0a5cfcf8edbf2ca2bb07a469ad361c612567cb949e326d52c77c39 (from https://www.piwheels.org/simple/biocode/) 2024-10-17T05:37:07,773 Skipping link: not a file: https://www.piwheels.org/simple/biocode/ 2024-10-17T05:37:07,774 Skipping link: not a file: https://pypi.org/simple/biocode/ 2024-10-17T05:37:07,795 Given no hashes to check 1 links for project 'biocode': discarding no candidates 2024-10-17T05:37:07,797 Collecting biocode==0.12.0 2024-10-17T05:37:07,799 Created temporary directory: /tmp/pip-unpack-ek6rx2cq 2024-10-17T05:37:07,897 Downloading biocode-0.12.0.tar.gz (6.5 MB) 2024-10-17T05:37:10,301 Added biocode==0.12.0 from https://files.pythonhosted.org/packages/76/b9/22a5ad1d471977fa223d22f5dfe57f099f1262fdd3fab678dfe555f11344/biocode-0.12.0.tar.gz to build tracker '/tmp/pip-build-tracker-23c3sqk5' 2024-10-17T05:37:10,303 Running setup.py (path:/tmp/pip-wheel-l06dwouk/biocode_952dfc81fcb64bcab9829c786a3cf82a/setup.py) egg_info for package biocode 2024-10-17T05:37:10,303 Created temporary directory: /tmp/pip-pip-egg-info-pxf16eph 2024-10-17T05:37:10,303 Preparing metadata (setup.py): started 2024-10-17T05:37:10,305 Running command python setup.py egg_info 2024-10-17T05:37:17,073 running egg_info 2024-10-17T05:37:17,074 creating /tmp/pip-pip-egg-info-pxf16eph/biocode.egg-info 2024-10-17T05:37:17,101 writing /tmp/pip-pip-egg-info-pxf16eph/biocode.egg-info/PKG-INFO 2024-10-17T05:37:17,106 writing dependency_links to /tmp/pip-pip-egg-info-pxf16eph/biocode.egg-info/dependency_links.txt 2024-10-17T05:37:17,108 writing requirements to /tmp/pip-pip-egg-info-pxf16eph/biocode.egg-info/requires.txt 2024-10-17T05:37:17,109 writing top-level names to /tmp/pip-pip-egg-info-pxf16eph/biocode.egg-info/top_level.txt 2024-10-17T05:37:17,110 writing manifest file '/tmp/pip-pip-egg-info-pxf16eph/biocode.egg-info/SOURCES.txt' 2024-10-17T05:37:17,238 reading manifest file '/tmp/pip-pip-egg-info-pxf16eph/biocode.egg-info/SOURCES.txt' 2024-10-17T05:37:17,240 reading manifest template 'MANIFEST.in' 2024-10-17T05:37:17,242 adding license file 'LICENSE' 2024-10-17T05:37:17,250 writing manifest file '/tmp/pip-pip-egg-info-pxf16eph/biocode.egg-info/SOURCES.txt' 2024-10-17T05:37:17,337 Preparing metadata (setup.py): finished with status 'done' 2024-10-17T05:37:17,343 Source in /tmp/pip-wheel-l06dwouk/biocode_952dfc81fcb64bcab9829c786a3cf82a has version 0.12.0, which satisfies requirement biocode==0.12.0 from https://files.pythonhosted.org/packages/76/b9/22a5ad1d471977fa223d22f5dfe57f099f1262fdd3fab678dfe555f11344/biocode-0.12.0.tar.gz 2024-10-17T05:37:17,344 Removed biocode==0.12.0 from https://files.pythonhosted.org/packages/76/b9/22a5ad1d471977fa223d22f5dfe57f099f1262fdd3fab678dfe555f11344/biocode-0.12.0.tar.gz from build tracker '/tmp/pip-build-tracker-23c3sqk5' 2024-10-17T05:37:17,351 Created temporary directory: /tmp/pip-unpack-hkanpsl0 2024-10-17T05:37:17,352 Created temporary directory: /tmp/pip-unpack-e30hpla4 2024-10-17T05:37:17,352 Building wheels for collected packages: biocode 2024-10-17T05:37:17,356 Created temporary directory: /tmp/pip-wheel-_cdmv8fa 2024-10-17T05:37:17,356 Building wheel for biocode (setup.py): started 2024-10-17T05:37:17,357 Destination directory: /tmp/pip-wheel-_cdmv8fa 2024-10-17T05:37:17,357 Running command python setup.py bdist_wheel 2024-10-17T05:37:18,249 running bdist_wheel 2024-10-17T05:37:18,380 running build 2024-10-17T05:37:18,380 running build_py 2024-10-17T05:37:18,410 creating build 2024-10-17T05:37:18,410 creating build/lib 2024-10-17T05:37:18,411 creating build/lib/biocode 2024-10-17T05:37:18,412 copying biocode/gff.py -> build/lib/biocode 2024-10-17T05:37:18,415 copying biocode/things.py -> build/lib/biocode 2024-10-17T05:37:18,418 copying biocode/utils.py -> build/lib/biocode 2024-10-17T05:37:18,420 copying biocode/genbank.py -> build/lib/biocode 2024-10-17T05:37:18,423 copying biocode/ncbigff.py -> build/lib/biocode 2024-10-17T05:37:18,425 copying biocode/annotation.py -> build/lib/biocode 2024-10-17T05:37:18,427 copying biocode/bed.py -> build/lib/biocode 2024-10-17T05:37:18,429 copying biocode/tbl.py -> build/lib/biocode 2024-10-17T05:37:18,431 copying biocode/__init__.py -> build/lib/biocode 2024-10-17T05:37:18,432 running egg_info 2024-10-17T05:37:18,458 writing biocode.egg-info/PKG-INFO 2024-10-17T05:37:18,462 writing dependency_links to biocode.egg-info/dependency_links.txt 2024-10-17T05:37:18,464 writing requirements to biocode.egg-info/requires.txt 2024-10-17T05:37:18,465 writing top-level names to biocode.egg-info/top_level.txt 2024-10-17T05:37:18,497 reading manifest file 'biocode.egg-info/SOURCES.txt' 2024-10-17T05:37:18,505 reading manifest template 'MANIFEST.in' 2024-10-17T05:37:18,507 adding license file 'LICENSE' 2024-10-17T05:37:18,516 writing manifest file 'biocode.egg-info/SOURCES.txt' 2024-10-17T05:37:18,521 /home/piwheels/.local/lib/python3.9/site-packages/setuptools/command/build_py.py:218: _Warning: Package 'biocode.data' is absent from the `packages` configuration. 2024-10-17T05:37:18,522 !! 2024-10-17T05:37:18,522 ******************************************************************************** 2024-10-17T05:37:18,522 ############################ 2024-10-17T05:37:18,522 # Package would be ignored # 2024-10-17T05:37:18,522 ############################ 2024-10-17T05:37:18,522 Python recognizes 'biocode.data' as an importable package[^1], 2024-10-17T05:37:18,523 but it is absent from setuptools' `packages` configuration. 2024-10-17T05:37:18,523 This leads to an ambiguous overall configuration. If you want to distribute this 2024-10-17T05:37:18,523 package, please make sure that 'biocode.data' is explicitly added 2024-10-17T05:37:18,523 to the `packages` configuration field. 2024-10-17T05:37:18,523 Alternatively, you can also rely on setuptools' discovery methods 2024-10-17T05:37:18,523 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-10-17T05:37:18,524 instead of `find_packages(...)`/`find:`). 2024-10-17T05:37:18,524 You can read more about "package discovery" on setuptools documentation page: 2024-10-17T05:37:18,524 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-10-17T05:37:18,524 If you don't want 'biocode.data' to be distributed and are 2024-10-17T05:37:18,525 already explicitly excluding 'biocode.data' via 2024-10-17T05:37:18,525 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-10-17T05:37:18,525 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-10-17T05:37:18,525 combination with a more fine grained `package-data` configuration. 2024-10-17T05:37:18,525 You can read more about "package data files" on setuptools documentation page: 2024-10-17T05:37:18,526 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-10-17T05:37:18,526 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-10-17T05:37:18,526 even if it does not contain any `.py` files. 2024-10-17T05:37:18,527 On the other hand, currently there is no concept of package data 2024-10-17T05:37:18,527 directory, all directories are treated like packages. 2024-10-17T05:37:18,527 ******************************************************************************** 2024-10-17T05:37:18,527 !! 2024-10-17T05:37:18,527 check.warn(importable) 2024-10-17T05:37:18,528 creating build/lib/biocode/data 2024-10-17T05:37:18,528 copying biocode/data/HMPslim.v2.1.obo -> build/lib/biocode/data 2024-10-17T05:37:18,528 copying biocode/data/__init__.py -> build/lib/biocode/data 2024-10-17T05:37:18,530 copying biocode/data/biocode_script_index.json -> build/lib/biocode/data 2024-10-17T05:37:18,532 copying biocode/data/genbank_flat_file_header.template -> build/lib/biocode/data 2024-10-17T05:37:18,534 copying biocode/data/go.obo -> build/lib/biocode/data 2024-10-17T05:37:19,044 copying biocode/data/go.pickle -> build/lib/biocode/data 2024-10-17T05:37:19,125 copying biocode/data/rsem_html_table.template -> build/lib/biocode/data 2024-10-17T05:37:19,128 running build_scripts 2024-10-17T05:37:19,129 creating build/scripts-3.9 2024-10-17T05:37:19,130 copying and adjusting bin/filter_fasta_by_type.py -> build/scripts-3.9 2024-10-17T05:37:19,132 copying and adjusting bin/uniref_to_sqlite3.py -> build/scripts-3.9 2024-10-17T05:37:19,134 copying and adjusting bin/uniprot_sprot_to_sqlite3.py -> build/scripts-3.9 2024-10-17T05:37:19,136 copying and adjusting bin/replace_homopolymeric_repeats_with_Ns.py -> build/scripts-3.9 2024-10-17T05:37:19,137 copying and adjusting bin/filter_fasta_by_abundance.py -> build/scripts-3.9 2024-10-17T05:37:19,139 copying and adjusting bin/add_gff3_locus_tags.py -> build/scripts-3.9 2024-10-17T05:37:19,141 copying and adjusting bin/detect_inverted_repeats.py -> build/scripts-3.9 2024-10-17T05:37:19,143 copying and adjusting bin/convert_blast_btab_to_bed.py -> build/scripts-3.9 2024-10-17T05:37:19,145 copying and adjusting bin/replace_gff_type_column_value.py -> build/scripts-3.9 2024-10-17T05:37:19,147 copying and adjusting bin/make_cufflinks_ids_unique.py -> build/scripts-3.9 2024-10-17T05:37:19,148 copying and adjusting bin/subsample_fasta.py -> build/scripts-3.9 2024-10-17T05:37:19,150 copying and adjusting bin/convert_cufflinks_gtf_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,152 copying and adjusting bin/report_or_replace_nonstandard_residues.py -> build/scripts-3.9 2024-10-17T05:37:19,154 copying and adjusting bin/convert_gff3_to_gbk.py -> build/scripts-3.9 2024-10-17T05:37:19,156 copying and adjusting bin/correct_gff3_CDS_phase_column.py -> build/scripts-3.9 2024-10-17T05:37:19,158 copying and adjusting bin/merge_bam_files.py -> build/scripts-3.9 2024-10-17T05:37:19,160 copying and adjusting bin/calculate_query_coverage_by_blast.py -> build/scripts-3.9 2024-10-17T05:37:19,162 copying and adjusting bin/get_mpilup_from_id_list.py -> build/scripts-3.9 2024-10-17T05:37:19,164 copying and adjusting bin/prepend_to_fasta_header.py -> build/scripts-3.9 2024-10-17T05:37:19,166 copying and adjusting bin/download_assemblies_from_genbank.py -> build/scripts-3.9 2024-10-17T05:37:19,169 copying and adjusting bin/remove_masked_gene_models.py -> build/scripts-3.9 2024-10-17T05:37:19,171 copying and adjusting bin/report_basic_gff_model_agreement.py -> build/scripts-3.9 2024-10-17T05:37:19,173 copying and adjusting bin/convert_scipio_gff_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,175 copying and adjusting bin/convert_gff3_to_ncbi_tbl.py -> build/scripts-3.9 2024-10-17T05:37:19,177 copying and adjusting bin/convert_pasa_gff_to_models.py -> build/scripts-3.9 2024-10-17T05:37:19,179 copying and adjusting bin/report_gff3_statistics.py -> build/scripts-3.9 2024-10-17T05:37:19,182 copying and adjusting bin/make_go_index.py -> build/scripts-3.9 2024-10-17T05:37:19,184 copying and adjusting bin/create_rsem_html_table.py -> build/scripts-3.9 2024-10-17T05:37:19,186 copying and adjusting bin/convert_htab_to_bed.py -> build/scripts-3.9 2024-10-17T05:37:19,188 copying and adjusting bin/convert_prodigal_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,190 copying and adjusting bin/add_polypeptide_to_gff3_gene_models.py -> build/scripts-3.9 2024-10-17T05:37:19,193 copying and adjusting bin/append_to_fasta_header.py -> build/scripts-3.9 2024-10-17T05:37:19,195 copying and adjusting bin/create_taxonomy_db.py -> build/scripts-3.9 2024-10-17T05:37:19,197 copying and adjusting bin/convert_genbank_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,200 copying and adjusting bin/merge_fasta_files_and_uniquify_ids.py -> build/scripts-3.9 2024-10-17T05:37:19,202 copying and adjusting bin/update_selected_column9_values.py -> build/scripts-3.9 2024-10-17T05:37:19,204 copying and adjusting bin/reverse_misordered_cds_coords.py -> build/scripts-3.9 2024-10-17T05:37:19,206 copying and adjusting bin/interleave_fastq.py -> build/scripts-3.9 2024-10-17T05:37:19,208 copying and adjusting bin/validate_feature_boundaries_on_molecules.py -> build/scripts-3.9 2024-10-17T05:37:19,210 copying and adjusting bin/report_go_slim_counts.py -> build/scripts-3.9 2024-10-17T05:37:19,212 copying and adjusting bin/tigrfam_info_to_sqlite3.py -> build/scripts-3.9 2024-10-17T05:37:19,215 copying and adjusting bin/report_gff_intron_and_intergenic_stats.py -> build/scripts-3.9 2024-10-17T05:37:19,217 copying and adjusting bin/select_training_and_evaluation_transcripts.py -> build/scripts-3.9 2024-10-17T05:37:19,219 copying and adjusting bin/reformat_fasta_residue_lengths.py -> build/scripts-3.9 2024-10-17T05:37:19,221 copying and adjusting bin/set_source_column.py -> build/scripts-3.9 2024-10-17T05:37:19,222 copying and adjusting bin/split_fasta_into_even_files.py -> build/scripts-3.9 2024-10-17T05:37:19,224 copying and adjusting bin/remove_duplicate_sequences.py -> build/scripts-3.9 2024-10-17T05:37:19,226 copying and adjusting bin/fasta_base_content.py -> build/scripts-3.9 2024-10-17T05:37:19,228 copying and adjusting bin/check_gff_for_internal_stops.py -> build/scripts-3.9 2024-10-17T05:37:19,229 copying and adjusting bin/convert_aat_btab_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,232 copying and adjusting bin/remove_orphaned_features.py -> build/scripts-3.9 2024-10-17T05:37:19,233 copying and adjusting bin/convert_gff_to_ncbi_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,235 copying and adjusting bin/convert_blast_btab_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,237 copying and adjusting bin/convert_glimmerHMM_gff_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,239 copying and adjusting bin/fastq_simple_stats.py -> build/scripts-3.9 2024-10-17T05:37:19,240 copying and adjusting bin/randomly_subsample_fastq.py -> build/scripts-3.9 2024-10-17T05:37:19,243 copying and adjusting bin/add_blast_results_to_gff3_product.py -> build/scripts-3.9 2024-10-17T05:37:19,245 copying and adjusting bin/fasta_simple_stats.py -> build/scripts-3.9 2024-10-17T05:37:19,247 copying and adjusting bin/split_interleaved_sequence_file.py -> build/scripts-3.9 2024-10-17T05:37:19,249 copying and adjusting bin/join_columnar_files.py -> build/scripts-3.9 2024-10-17T05:37:19,250 copying and adjusting bin/merge_masked_fasta_files.py -> build/scripts-3.9 2024-10-17T05:37:19,252 copying and adjusting bin/check_for_embedded_fasta_headers.py -> build/scripts-3.9 2024-10-17T05:37:19,254 copying and adjusting bin/filter_gff3_by_id_list.py -> build/scripts-3.9 2024-10-17T05:37:19,256 copying and adjusting bin/convert_stringtie_gtf_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,258 copying and adjusting bin/validate_fasta.py -> build/scripts-3.9 2024-10-17T05:37:19,260 copying and adjusting bin/remove_fasta_from_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,262 copying and adjusting bin/fasta_size_report.py -> build/scripts-3.9 2024-10-17T05:37:19,264 copying and adjusting bin/merge_predicted_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,266 copying and adjusting bin/append_to_fastq_read_header.py -> build/scripts-3.9 2024-10-17T05:37:19,267 copying and adjusting bin/fasta_size_distribution_plot.py -> build/scripts-3.9 2024-10-17T05:37:19,269 copying and adjusting bin/convert_fastq_to_fasta.py -> build/scripts-3.9 2024-10-17T05:37:19,271 copying and adjusting bin/eggnog_to_sqlite3.py -> build/scripts-3.9 2024-10-17T05:37:19,273 copying and adjusting bin/mark_partial_genes.py -> build/scripts-3.9 2024-10-17T05:37:19,275 copying and adjusting bin/validate_mate_pairing.py -> build/scripts-3.9 2024-10-17T05:37:19,277 copying and adjusting bin/convert_metagenemark_gff_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,279 copying and adjusting bin/hmmlib_to_sqlite3.py -> build/scripts-3.9 2024-10-17T05:37:19,281 copying and adjusting bin/convert_fasta_contigs_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,283 copying and adjusting bin/convert_cegma_gff_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,285 copying and adjusting bin/append_to_column_9_value.py -> build/scripts-3.9 2024-10-17T05:37:19,287 copying and adjusting bin/make_go_slim_index.py -> build/scripts-3.9 2024-10-17T05:37:19,289 copying and adjusting bin/convert_gff3_to_gene_association_format.py -> build/scripts-3.9 2024-10-17T05:37:19,291 copying and adjusting bin/reorient_sequences_by_id.py -> build/scripts-3.9 2024-10-17T05:37:19,292 copying and adjusting bin/report_matrix_shape.py -> build/scripts-3.9 2024-10-17T05:37:19,294 copying and adjusting bin/make_go_slim.py -> build/scripts-3.9 2024-10-17T05:37:19,296 copying and adjusting bin/extract_fasta_regions.py -> build/scripts-3.9 2024-10-17T05:37:19,298 copying and adjusting bin/filter_fastq_by_N_content.py -> build/scripts-3.9 2024-10-17T05:37:19,300 copying and adjusting bin/filter_fasta_by_header_regex.py -> build/scripts-3.9 2024-10-17T05:37:19,302 copying and adjusting bin/filter_uniref_by_taxonomy.py -> build/scripts-3.9 2024-10-17T05:37:19,304 copying and adjusting bin/create_taxonomic_profile_from_blast.py -> build/scripts-3.9 2024-10-17T05:37:19,307 copying and adjusting bin/split_molecules_on_gaps.py -> build/scripts-3.9 2024-10-17T05:37:19,308 copying and adjusting bin/remove_duplicate_features.py -> build/scripts-3.9 2024-10-17T05:37:19,310 copying and adjusting bin/convert_gff3_to_bed.py -> build/scripts-3.9 2024-10-17T05:37:19,312 copying and adjusting bin/export_fasta_ids.py -> build/scripts-3.9 2024-10-17T05:37:19,313 copying and adjusting bin/list_biocode.py -> build/scripts-3.9 2024-10-17T05:37:19,315 copying and adjusting bin/split_isoforms_into_individual_genes.py -> build/scripts-3.9 2024-10-17T05:37:19,316 copying and adjusting bin/interleave_fasta.py -> build/scripts-3.9 2024-10-17T05:37:19,318 copying and adjusting bin/strip_fasta_headers_after_regex.py -> build/scripts-3.9 2024-10-17T05:37:19,319 copying and adjusting bin/convert_augustus_to_gff3.py -> build/scripts-3.9 2024-10-17T05:37:19,321 copying and adjusting bin/filter_uniref_by_repid.py -> build/scripts-3.9 2024-10-17T05:37:19,323 copying and adjusting bin/extend_genes_to_stops.py -> build/scripts-3.9 2024-10-17T05:37:19,325 copying and adjusting bin/compare_gene_structures.py -> build/scripts-3.9 2024-10-17T05:37:19,328 copying and adjusting bin/write_fasta_from_gff.py -> build/scripts-3.9 2024-10-17T05:37:19,330 copying and adjusting bin/calculate_gene_coverage_from_assembly.py -> build/scripts-3.9 2024-10-17T05:37:19,332 copying and adjusting bin/report_coverage_gaps.py -> build/scripts-3.9 2024-10-17T05:37:19,334 changing mode of build/scripts-3.9/filter_fasta_by_type.py from 644 to 755 2024-10-17T05:37:19,334 changing mode of build/scripts-3.9/uniref_to_sqlite3.py from 644 to 755 2024-10-17T05:37:19,334 changing mode of build/scripts-3.9/uniprot_sprot_to_sqlite3.py from 644 to 755 2024-10-17T05:37:19,335 changing mode of build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py from 644 to 755 2024-10-17T05:37:19,335 changing mode of build/scripts-3.9/filter_fasta_by_abundance.py from 644 to 755 2024-10-17T05:37:19,336 changing mode of build/scripts-3.9/add_gff3_locus_tags.py from 644 to 755 2024-10-17T05:37:19,336 changing mode of build/scripts-3.9/detect_inverted_repeats.py from 644 to 755 2024-10-17T05:37:19,336 changing mode of build/scripts-3.9/convert_blast_btab_to_bed.py from 644 to 755 2024-10-17T05:37:19,337 changing mode of build/scripts-3.9/replace_gff_type_column_value.py from 644 to 755 2024-10-17T05:37:19,337 changing mode of build/scripts-3.9/make_cufflinks_ids_unique.py from 644 to 755 2024-10-17T05:37:19,337 changing mode of build/scripts-3.9/subsample_fasta.py from 644 to 755 2024-10-17T05:37:19,338 changing mode of build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py from 644 to 755 2024-10-17T05:37:19,338 changing mode of build/scripts-3.9/report_or_replace_nonstandard_residues.py from 644 to 755 2024-10-17T05:37:19,338 changing mode of build/scripts-3.9/convert_gff3_to_gbk.py from 644 to 755 2024-10-17T05:37:19,339 changing mode of build/scripts-3.9/correct_gff3_CDS_phase_column.py from 644 to 755 2024-10-17T05:37:19,339 changing mode of build/scripts-3.9/merge_bam_files.py from 644 to 755 2024-10-17T05:37:19,339 changing mode of build/scripts-3.9/calculate_query_coverage_by_blast.py from 644 to 755 2024-10-17T05:37:19,340 changing mode of build/scripts-3.9/get_mpilup_from_id_list.py from 644 to 755 2024-10-17T05:37:19,340 changing mode of build/scripts-3.9/prepend_to_fasta_header.py from 644 to 755 2024-10-17T05:37:19,341 changing mode of build/scripts-3.9/download_assemblies_from_genbank.py from 644 to 755 2024-10-17T05:37:19,341 changing mode of build/scripts-3.9/remove_masked_gene_models.py from 644 to 755 2024-10-17T05:37:19,341 changing mode of build/scripts-3.9/report_basic_gff_model_agreement.py from 644 to 755 2024-10-17T05:37:19,342 changing mode of build/scripts-3.9/convert_scipio_gff_to_gff3.py from 644 to 755 2024-10-17T05:37:19,342 changing mode of build/scripts-3.9/convert_gff3_to_ncbi_tbl.py from 644 to 755 2024-10-17T05:37:19,342 changing mode of build/scripts-3.9/convert_pasa_gff_to_models.py from 644 to 755 2024-10-17T05:37:19,343 changing mode of build/scripts-3.9/report_gff3_statistics.py from 644 to 755 2024-10-17T05:37:19,343 changing mode of build/scripts-3.9/make_go_index.py from 644 to 755 2024-10-17T05:37:19,343 changing mode of build/scripts-3.9/create_rsem_html_table.py from 644 to 755 2024-10-17T05:37:19,344 changing mode of build/scripts-3.9/convert_htab_to_bed.py from 644 to 755 2024-10-17T05:37:19,344 changing mode of build/scripts-3.9/convert_prodigal_to_gff3.py from 644 to 755 2024-10-17T05:37:19,345 changing mode of build/scripts-3.9/add_polypeptide_to_gff3_gene_models.py from 644 to 755 2024-10-17T05:37:19,345 changing mode of build/scripts-3.9/append_to_fasta_header.py from 644 to 755 2024-10-17T05:37:19,345 changing mode of build/scripts-3.9/create_taxonomy_db.py from 644 to 755 2024-10-17T05:37:19,346 changing mode of build/scripts-3.9/convert_genbank_to_gff3.py from 644 to 755 2024-10-17T05:37:19,346 changing mode of build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py from 644 to 755 2024-10-17T05:37:19,346 changing mode of build/scripts-3.9/update_selected_column9_values.py from 644 to 755 2024-10-17T05:37:19,347 changing mode of build/scripts-3.9/reverse_misordered_cds_coords.py from 644 to 755 2024-10-17T05:37:19,347 changing mode of build/scripts-3.9/interleave_fastq.py from 644 to 755 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changing mode of build/scripts-3.9/fasta_base_content.py from 644 to 755 2024-10-17T05:37:19,351 changing mode of build/scripts-3.9/check_gff_for_internal_stops.py from 644 to 755 2024-10-17T05:37:19,351 changing mode of build/scripts-3.9/convert_aat_btab_to_gff3.py from 644 to 755 2024-10-17T05:37:19,352 changing mode of build/scripts-3.9/remove_orphaned_features.py from 644 to 755 2024-10-17T05:37:19,352 changing mode of build/scripts-3.9/convert_gff_to_ncbi_gff3.py from 644 to 755 2024-10-17T05:37:19,352 changing mode of build/scripts-3.9/convert_blast_btab_to_gff3.py from 644 to 755 2024-10-17T05:37:19,353 changing mode of build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py from 644 to 755 2024-10-17T05:37:19,353 changing mode of build/scripts-3.9/fastq_simple_stats.py from 644 to 755 2024-10-17T05:37:19,353 changing mode of build/scripts-3.9/randomly_subsample_fastq.py from 644 to 755 2024-10-17T05:37:19,354 changing mode of build/scripts-3.9/add_blast_results_to_gff3_product.py from 644 to 755 2024-10-17T05:37:19,354 changing mode of build/scripts-3.9/fasta_simple_stats.py from 644 to 755 2024-10-17T05:37:19,354 changing mode of build/scripts-3.9/split_interleaved_sequence_file.py from 644 to 755 2024-10-17T05:37:19,355 changing mode of build/scripts-3.9/join_columnar_files.py from 644 to 755 2024-10-17T05:37:19,355 changing mode of build/scripts-3.9/merge_masked_fasta_files.py from 644 to 755 2024-10-17T05:37:19,355 changing mode of build/scripts-3.9/check_for_embedded_fasta_headers.py from 644 to 755 2024-10-17T05:37:19,356 changing mode of build/scripts-3.9/filter_gff3_by_id_list.py from 644 to 755 2024-10-17T05:37:19,356 changing mode of build/scripts-3.9/convert_stringtie_gtf_to_gff3.py from 644 to 755 2024-10-17T05:37:19,356 changing mode of build/scripts-3.9/validate_fasta.py from 644 to 755 2024-10-17T05:37:19,357 changing mode of build/scripts-3.9/remove_fasta_from_gff3.py from 644 to 755 2024-10-17T05:37:19,357 changing mode of build/scripts-3.9/fasta_size_report.py from 644 to 755 2024-10-17T05:37:19,357 changing mode of build/scripts-3.9/merge_predicted_gff3.py from 644 to 755 2024-10-17T05:37:19,358 changing mode of build/scripts-3.9/append_to_fastq_read_header.py from 644 to 755 2024-10-17T05:37:19,358 changing mode of build/scripts-3.9/fasta_size_distribution_plot.py from 644 to 755 2024-10-17T05:37:19,358 changing mode of build/scripts-3.9/convert_fastq_to_fasta.py from 644 to 755 2024-10-17T05:37:19,359 changing mode of build/scripts-3.9/eggnog_to_sqlite3.py from 644 to 755 2024-10-17T05:37:19,359 changing mode of build/scripts-3.9/mark_partial_genes.py from 644 to 755 2024-10-17T05:37:19,359 changing mode of build/scripts-3.9/validate_mate_pairing.py from 644 to 755 2024-10-17T05:37:19,360 changing mode of build/scripts-3.9/convert_metagenemark_gff_to_gff3.py from 644 to 755 2024-10-17T05:37:19,360 changing mode of build/scripts-3.9/hmmlib_to_sqlite3.py from 644 to 755 2024-10-17T05:37:19,361 changing mode of build/scripts-3.9/convert_fasta_contigs_to_gff3.py from 644 to 755 2024-10-17T05:37:19,361 changing mode of build/scripts-3.9/convert_cegma_gff_to_gff3.py from 644 to 755 2024-10-17T05:37:19,361 changing mode of build/scripts-3.9/append_to_column_9_value.py from 644 to 755 2024-10-17T05:37:19,362 changing mode of build/scripts-3.9/make_go_slim_index.py from 644 to 755 2024-10-17T05:37:19,362 changing mode of build/scripts-3.9/convert_gff3_to_gene_association_format.py from 644 to 755 2024-10-17T05:37:19,362 changing mode of build/scripts-3.9/reorient_sequences_by_id.py from 644 to 755 2024-10-17T05:37:19,363 changing mode of build/scripts-3.9/report_matrix_shape.py from 644 to 755 2024-10-17T05:37:19,363 changing mode of build/scripts-3.9/make_go_slim.py from 644 to 755 2024-10-17T05:37:19,363 changing mode of build/scripts-3.9/extract_fasta_regions.py from 644 to 755 2024-10-17T05:37:19,364 changing mode of build/scripts-3.9/filter_fastq_by_N_content.py from 644 to 755 2024-10-17T05:37:19,364 changing mode of build/scripts-3.9/filter_fasta_by_header_regex.py from 644 to 755 2024-10-17T05:37:19,364 changing mode of build/scripts-3.9/filter_uniref_by_taxonomy.py from 644 to 755 2024-10-17T05:37:19,365 changing mode of build/scripts-3.9/create_taxonomic_profile_from_blast.py from 644 to 755 2024-10-17T05:37:19,365 changing mode of build/scripts-3.9/split_molecules_on_gaps.py from 644 to 755 2024-10-17T05:37:19,365 changing mode of build/scripts-3.9/remove_duplicate_features.py from 644 to 755 2024-10-17T05:37:19,366 changing mode of build/scripts-3.9/convert_gff3_to_bed.py from 644 to 755 2024-10-17T05:37:19,366 changing mode of build/scripts-3.9/export_fasta_ids.py from 644 to 755 2024-10-17T05:37:19,366 changing mode of build/scripts-3.9/list_biocode.py from 644 to 755 2024-10-17T05:37:19,367 changing mode of build/scripts-3.9/split_isoforms_into_individual_genes.py from 644 to 755 2024-10-17T05:37:19,367 changing mode of build/scripts-3.9/interleave_fasta.py from 644 to 755 2024-10-17T05:37:19,367 changing mode of build/scripts-3.9/strip_fasta_headers_after_regex.py from 644 to 755 2024-10-17T05:37:19,368 changing mode of build/scripts-3.9/convert_augustus_to_gff3.py from 644 to 755 2024-10-17T05:37:19,368 changing mode of build/scripts-3.9/filter_uniref_by_repid.py from 644 to 755 2024-10-17T05:37:19,368 changing mode of build/scripts-3.9/extend_genes_to_stops.py from 644 to 755 2024-10-17T05:37:19,369 changing mode of build/scripts-3.9/compare_gene_structures.py from 644 to 755 2024-10-17T05:37:19,369 changing mode of build/scripts-3.9/write_fasta_from_gff.py from 644 to 755 2024-10-17T05:37:19,369 changing mode of build/scripts-3.9/calculate_gene_coverage_from_assembly.py from 644 to 755 2024-10-17T05:37:19,370 changing mode of build/scripts-3.9/report_coverage_gaps.py from 644 to 755 2024-10-17T05:37:19,396 /home/piwheels/.local/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-10-17T05:37:19,396 !! 2024-10-17T05:37:19,397 ******************************************************************************** 2024-10-17T05:37:19,397 Please avoid running ``setup.py`` directly. 2024-10-17T05:37:19,397 Instead, use pypa/build, pypa/installer or other 2024-10-17T05:37:19,397 standards-based tools. 2024-10-17T05:37:19,397 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-10-17T05:37:19,397 ******************************************************************************** 2024-10-17T05:37:19,398 !! 2024-10-17T05:37:19,398 self.initialize_options() 2024-10-17T05:37:19,422 installing to build/bdist.linux-armv7l/wheel 2024-10-17T05:37:19,422 running install 2024-10-17T05:37:19,447 running install_lib 2024-10-17T05:37:19,473 creating build/bdist.linux-armv7l 2024-10-17T05:37:19,474 creating build/bdist.linux-armv7l/wheel 2024-10-17T05:37:19,475 creating build/bdist.linux-armv7l/wheel/biocode 2024-10-17T05:37:19,476 copying build/lib/biocode/gff.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:19,479 copying build/lib/biocode/things.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:19,482 copying build/lib/biocode/utils.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:19,485 creating build/bdist.linux-armv7l/wheel/biocode/data 2024-10-17T05:37:19,486 copying build/lib/biocode/data/rsem_html_table.template -> build/bdist.linux-armv7l/wheel/./biocode/data 2024-10-17T05:37:19,489 copying build/lib/biocode/data/genbank_flat_file_header.template -> build/bdist.linux-armv7l/wheel/./biocode/data 2024-10-17T05:37:19,491 copying build/lib/biocode/data/go.obo -> build/bdist.linux-armv7l/wheel/./biocode/data 2024-10-17T05:37:20,820 copying build/lib/biocode/data/biocode_script_index.json -> build/bdist.linux-armv7l/wheel/./biocode/data 2024-10-17T05:37:20,823 copying build/lib/biocode/data/go.pickle -> build/bdist.linux-armv7l/wheel/./biocode/data 2024-10-17T05:37:21,009 copying build/lib/biocode/data/__init__.py -> build/bdist.linux-armv7l/wheel/./biocode/data 2024-10-17T05:37:21,011 copying build/lib/biocode/data/HMPslim.v2.1.obo -> build/bdist.linux-armv7l/wheel/./biocode/data 2024-10-17T05:37:21,016 copying build/lib/biocode/genbank.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:21,019 copying build/lib/biocode/ncbigff.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:21,022 copying build/lib/biocode/annotation.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:21,025 copying build/lib/biocode/bed.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:21,034 copying build/lib/biocode/tbl.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:21,038 copying build/lib/biocode/__init__.py -> build/bdist.linux-armv7l/wheel/./biocode 2024-10-17T05:37:21,039 running install_egg_info 2024-10-17T05:37:21,105 Copying biocode.egg-info to build/bdist.linux-armv7l/wheel/./biocode-0.12.0-py3.9.egg-info 2024-10-17T05:37:21,138 running install_scripts 2024-10-17T05:37:21,144 creating build/bdist.linux-armv7l/wheel/biocode-0.12.0.data 2024-10-17T05:37:21,145 creating build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,146 copying build/scripts-3.9/randomly_subsample_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,149 copying build/scripts-3.9/split_interleaved_sequence_file.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,152 copying build/scripts-3.9/append_to_column_9_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,154 copying build/scripts-3.9/mark_partial_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,157 copying build/scripts-3.9/tigrfam_info_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,162 copying build/scripts-3.9/filter_gff3_by_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,165 copying build/scripts-3.9/join_columnar_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,167 copying build/scripts-3.9/fasta_size_distribution_plot.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,170 copying build/scripts-3.9/extract_fasta_regions.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,175 copying build/scripts-3.9/filter_fasta_by_type.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,177 copying build/scripts-3.9/filter_uniref_by_taxonomy.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,180 copying build/scripts-3.9/convert_gff3_to_ncbi_tbl.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,183 copying build/scripts-3.9/correct_gff3_CDS_phase_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,186 copying build/scripts-3.9/reverse_misordered_cds_coords.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,188 copying build/scripts-3.9/convert_htab_to_bed.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,191 copying build/scripts-3.9/hmmlib_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,194 copying build/scripts-3.9/convert_fastq_to_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,197 copying build/scripts-3.9/compare_gene_structures.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,200 copying build/scripts-3.9/report_or_replace_nonstandard_residues.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,203 copying build/scripts-3.9/subsample_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,205 copying build/scripts-3.9/uniprot_sprot_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,208 copying build/scripts-3.9/split_isoforms_into_individual_genes.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,211 copying build/scripts-3.9/interleave_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,213 copying build/scripts-3.9/remove_fasta_from_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,215 copying build/scripts-3.9/convert_scipio_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,218 copying build/scripts-3.9/convert_cegma_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,221 copying build/scripts-3.9/convert_prodigal_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,224 copying build/scripts-3.9/export_fasta_ids.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,227 copying build/scripts-3.9/replace_homopolymeric_repeats_with_Ns.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,229 copying build/scripts-3.9/write_fasta_from_gff.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,232 copying build/scripts-3.9/convert_gff_to_ncbi_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,235 copying build/scripts-3.9/convert_glimmerHMM_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,238 copying build/scripts-3.9/add_gff3_locus_tags.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,240 copying build/scripts-3.9/make_go_slim_index.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,243 copying build/scripts-3.9/make_go_slim.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,246 copying build/scripts-3.9/download_assemblies_from_genbank.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,249 copying build/scripts-3.9/validate_mate_pairing.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,252 copying build/scripts-3.9/convert_augustus_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,255 copying build/scripts-3.9/remove_orphaned_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,257 copying build/scripts-3.9/report_gff3_statistics.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,260 copying build/scripts-3.9/convert_blast_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,263 copying build/scripts-3.9/split_fasta_into_even_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,265 copying build/scripts-3.9/report_go_slim_counts.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,268 copying build/scripts-3.9/filter_fasta_by_header_regex.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,270 copying build/scripts-3.9/fasta_simple_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,273 copying build/scripts-3.9/filter_fastq_by_N_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,276 copying build/scripts-3.9/create_taxonomic_profile_from_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,279 copying build/scripts-3.9/select_training_and_evaluation_transcripts.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,282 copying build/scripts-3.9/set_source_column.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,285 copying build/scripts-3.9/convert_aat_btab_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,289 copying build/scripts-3.9/convert_gff3_to_gbk.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,293 copying build/scripts-3.9/strip_fasta_headers_after_regex.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,300 copying build/scripts-3.9/eggnog_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,303 copying build/scripts-3.9/report_gff_intron_and_intergenic_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,306 copying build/scripts-3.9/remove_duplicate_sequences.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,317 copying build/scripts-3.9/convert_gff3_to_gene_association_format.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,320 copying build/scripts-3.9/reorient_sequences_by_id.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,323 copying build/scripts-3.9/create_rsem_html_table.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,326 copying build/scripts-3.9/validate_fasta.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,329 copying build/scripts-3.9/fasta_base_content.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,331 copying build/scripts-3.9/append_to_fastq_read_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,334 copying build/scripts-3.9/report_coverage_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,337 copying build/scripts-3.9/interleave_fastq.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,341 copying build/scripts-3.9/reformat_fasta_residue_lengths.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,344 copying build/scripts-3.9/merge_predicted_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,348 copying build/scripts-3.9/list_biocode.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,350 copying build/scripts-3.9/add_blast_results_to_gff3_product.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,353 copying build/scripts-3.9/convert_fasta_contigs_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,356 copying build/scripts-3.9/fasta_size_report.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,359 copying build/scripts-3.9/update_selected_column9_values.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,362 copying build/scripts-3.9/add_polypeptide_to_gff3_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,365 copying build/scripts-3.9/merge_masked_fasta_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,368 copying build/scripts-3.9/extend_genes_to_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,371 copying build/scripts-3.9/prepend_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,374 copying build/scripts-3.9/filter_uniref_by_repid.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,376 copying build/scripts-3.9/replace_gff_type_column_value.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,379 copying build/scripts-3.9/filter_fasta_by_abundance.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,381 copying build/scripts-3.9/append_to_fasta_header.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,383 copying build/scripts-3.9/check_gff_for_internal_stops.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,386 copying build/scripts-3.9/convert_genbank_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,390 copying build/scripts-3.9/remove_masked_gene_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,393 copying build/scripts-3.9/create_taxonomy_db.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,396 copying build/scripts-3.9/fastq_simple_stats.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,399 copying build/scripts-3.9/report_basic_gff_model_agreement.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,401 copying build/scripts-3.9/uniref_to_sqlite3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,404 copying build/scripts-3.9/make_go_index.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,407 copying build/scripts-3.9/calculate_gene_coverage_from_assembly.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,410 copying build/scripts-3.9/convert_pasa_gff_to_models.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,413 copying build/scripts-3.9/validate_feature_boundaries_on_molecules.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,415 copying build/scripts-3.9/convert_metagenemark_gff_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,418 copying build/scripts-3.9/make_cufflinks_ids_unique.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,421 copying build/scripts-3.9/split_molecules_on_gaps.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,423 copying build/scripts-3.9/convert_blast_btab_to_bed.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,426 copying build/scripts-3.9/check_for_embedded_fasta_headers.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,428 copying build/scripts-3.9/calculate_query_coverage_by_blast.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,431 copying build/scripts-3.9/convert_cufflinks_gtf_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,434 copying build/scripts-3.9/convert_gff3_to_bed.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,436 copying build/scripts-3.9/merge_bam_files.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,439 copying build/scripts-3.9/get_mpilup_from_id_list.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,441 copying build/scripts-3.9/merge_fasta_files_and_uniquify_ids.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,444 copying build/scripts-3.9/detect_inverted_repeats.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,447 copying build/scripts-3.9/convert_stringtie_gtf_to_gff3.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,449 copying build/scripts-3.9/remove_duplicate_features.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,451 copying build/scripts-3.9/report_matrix_shape.py -> build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts 2024-10-17T05:37:21,453 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/randomly_subsample_fastq.py to 755 2024-10-17T05:37:21,453 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/split_interleaved_sequence_file.py to 755 2024-10-17T05:37:21,454 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/append_to_column_9_value.py to 755 2024-10-17T05:37:21,454 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/mark_partial_genes.py to 755 2024-10-17T05:37:21,454 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/tigrfam_info_to_sqlite3.py to 755 2024-10-17T05:37:21,455 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/filter_gff3_by_id_list.py to 755 2024-10-17T05:37:21,455 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/join_columnar_files.py to 755 2024-10-17T05:37:21,455 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/fasta_size_distribution_plot.py to 755 2024-10-17T05:37:21,456 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/extract_fasta_regions.py to 755 2024-10-17T05:37:21,456 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/filter_fasta_by_type.py to 755 2024-10-17T05:37:21,457 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/filter_uniref_by_taxonomy.py to 755 2024-10-17T05:37:21,457 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_gff3_to_ncbi_tbl.py to 755 2024-10-17T05:37:21,457 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/correct_gff3_CDS_phase_column.py to 755 2024-10-17T05:37:21,458 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/reverse_misordered_cds_coords.py to 755 2024-10-17T05:37:21,458 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_htab_to_bed.py to 755 2024-10-17T05:37:21,458 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/hmmlib_to_sqlite3.py to 755 2024-10-17T05:37:21,459 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_fastq_to_fasta.py to 755 2024-10-17T05:37:21,459 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/compare_gene_structures.py to 755 2024-10-17T05:37:21,459 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/report_or_replace_nonstandard_residues.py to 755 2024-10-17T05:37:21,460 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/subsample_fasta.py to 755 2024-10-17T05:37:21,460 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/uniprot_sprot_to_sqlite3.py to 755 2024-10-17T05:37:21,461 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/split_isoforms_into_individual_genes.py to 755 2024-10-17T05:37:21,461 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/interleave_fasta.py to 755 2024-10-17T05:37:21,461 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/remove_fasta_from_gff3.py to 755 2024-10-17T05:37:21,462 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_scipio_gff_to_gff3.py to 755 2024-10-17T05:37:21,462 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_cegma_gff_to_gff3.py to 755 2024-10-17T05:37:21,462 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_prodigal_to_gff3.py to 755 2024-10-17T05:37:21,463 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/export_fasta_ids.py to 755 2024-10-17T05:37:21,463 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/replace_homopolymeric_repeats_with_Ns.py to 755 2024-10-17T05:37:21,463 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/write_fasta_from_gff.py to 755 2024-10-17T05:37:21,464 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_gff_to_ncbi_gff3.py to 755 2024-10-17T05:37:21,464 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_glimmerHMM_gff_to_gff3.py to 755 2024-10-17T05:37:21,465 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/add_gff3_locus_tags.py to 755 2024-10-17T05:37:21,465 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/make_go_slim_index.py to 755 2024-10-17T05:37:21,465 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/make_go_slim.py to 755 2024-10-17T05:37:21,466 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/download_assemblies_from_genbank.py to 755 2024-10-17T05:37:21,466 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/validate_mate_pairing.py to 755 2024-10-17T05:37:21,466 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_augustus_to_gff3.py to 755 2024-10-17T05:37:21,467 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/remove_orphaned_features.py to 755 2024-10-17T05:37:21,467 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/report_gff3_statistics.py to 755 2024-10-17T05:37:21,467 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_blast_btab_to_gff3.py to 755 2024-10-17T05:37:21,468 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/split_fasta_into_even_files.py to 755 2024-10-17T05:37:21,468 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/report_go_slim_counts.py to 755 2024-10-17T05:37:21,469 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/filter_fasta_by_header_regex.py to 755 2024-10-17T05:37:21,470 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/fasta_simple_stats.py to 755 2024-10-17T05:37:21,470 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/filter_fastq_by_N_content.py to 755 2024-10-17T05:37:21,470 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/create_taxonomic_profile_from_blast.py to 755 2024-10-17T05:37:21,471 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/select_training_and_evaluation_transcripts.py to 755 2024-10-17T05:37:21,471 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/set_source_column.py to 755 2024-10-17T05:37:21,471 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_aat_btab_to_gff3.py to 755 2024-10-17T05:37:21,472 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_gff3_to_gbk.py to 755 2024-10-17T05:37:21,472 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/strip_fasta_headers_after_regex.py to 755 2024-10-17T05:37:21,473 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/eggnog_to_sqlite3.py to 755 2024-10-17T05:37:21,473 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/report_gff_intron_and_intergenic_stats.py to 755 2024-10-17T05:37:21,474 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/remove_duplicate_sequences.py to 755 2024-10-17T05:37:21,474 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_gff3_to_gene_association_format.py to 755 2024-10-17T05:37:21,474 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/reorient_sequences_by_id.py to 755 2024-10-17T05:37:21,475 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/create_rsem_html_table.py to 755 2024-10-17T05:37:21,475 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/validate_fasta.py to 755 2024-10-17T05:37:21,475 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/fasta_base_content.py to 755 2024-10-17T05:37:21,476 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/append_to_fastq_read_header.py to 755 2024-10-17T05:37:21,476 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/report_coverage_gaps.py to 755 2024-10-17T05:37:21,477 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/interleave_fastq.py to 755 2024-10-17T05:37:21,477 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/reformat_fasta_residue_lengths.py to 755 2024-10-17T05:37:21,477 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/merge_predicted_gff3.py to 755 2024-10-17T05:37:21,478 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/list_biocode.py to 755 2024-10-17T05:37:21,478 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/add_blast_results_to_gff3_product.py to 755 2024-10-17T05:37:21,479 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_fasta_contigs_to_gff3.py to 755 2024-10-17T05:37:21,479 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/fasta_size_report.py to 755 2024-10-17T05:37:21,479 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/update_selected_column9_values.py to 755 2024-10-17T05:37:21,480 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/add_polypeptide_to_gff3_gene_models.py to 755 2024-10-17T05:37:21,480 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/merge_masked_fasta_files.py to 755 2024-10-17T05:37:21,480 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/extend_genes_to_stops.py to 755 2024-10-17T05:37:21,481 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/prepend_to_fasta_header.py to 755 2024-10-17T05:37:21,481 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/filter_uniref_by_repid.py to 755 2024-10-17T05:37:21,481 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/replace_gff_type_column_value.py to 755 2024-10-17T05:37:21,482 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/filter_fasta_by_abundance.py to 755 2024-10-17T05:37:21,482 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/append_to_fasta_header.py to 755 2024-10-17T05:37:21,483 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/check_gff_for_internal_stops.py to 755 2024-10-17T05:37:21,483 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_genbank_to_gff3.py to 755 2024-10-17T05:37:21,484 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/remove_masked_gene_models.py to 755 2024-10-17T05:37:21,484 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/create_taxonomy_db.py to 755 2024-10-17T05:37:21,485 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/fastq_simple_stats.py to 755 2024-10-17T05:37:21,485 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/report_basic_gff_model_agreement.py to 755 2024-10-17T05:37:21,486 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/uniref_to_sqlite3.py to 755 2024-10-17T05:37:21,486 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/make_go_index.py to 755 2024-10-17T05:37:21,486 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/calculate_gene_coverage_from_assembly.py to 755 2024-10-17T05:37:21,487 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_pasa_gff_to_models.py to 755 2024-10-17T05:37:21,487 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/validate_feature_boundaries_on_molecules.py to 755 2024-10-17T05:37:21,487 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_metagenemark_gff_to_gff3.py to 755 2024-10-17T05:37:21,488 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/make_cufflinks_ids_unique.py to 755 2024-10-17T05:37:21,488 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/split_molecules_on_gaps.py to 755 2024-10-17T05:37:21,489 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_blast_btab_to_bed.py to 755 2024-10-17T05:37:21,489 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/check_for_embedded_fasta_headers.py to 755 2024-10-17T05:37:21,490 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/calculate_query_coverage_by_blast.py to 755 2024-10-17T05:37:21,490 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_cufflinks_gtf_to_gff3.py to 755 2024-10-17T05:37:21,490 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_gff3_to_bed.py to 755 2024-10-17T05:37:21,491 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/merge_bam_files.py to 755 2024-10-17T05:37:21,491 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/get_mpilup_from_id_list.py to 755 2024-10-17T05:37:21,491 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/merge_fasta_files_and_uniquify_ids.py to 755 2024-10-17T05:37:21,492 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/detect_inverted_repeats.py to 755 2024-10-17T05:37:21,492 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/convert_stringtie_gtf_to_gff3.py to 755 2024-10-17T05:37:21,493 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/remove_duplicate_features.py to 755 2024-10-17T05:37:21,493 changing mode of build/bdist.linux-armv7l/wheel/biocode-0.12.0.data/scripts/report_matrix_shape.py to 755 2024-10-17T05:37:21,510 creating build/bdist.linux-armv7l/wheel/biocode-0.12.0.dist-info/WHEEL 2024-10-17T05:37:21,512 creating '/tmp/pip-wheel-_cdmv8fa/biocode-0.12.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-10-17T05:37:21,515 adding 'biocode/__init__.py' 2024-10-17T05:37:21,518 adding 'biocode/annotation.py' 2024-10-17T05:37:21,520 adding 'biocode/bed.py' 2024-10-17T05:37:21,522 adding 'biocode/genbank.py' 2024-10-17T05:37:21,527 adding 'biocode/gff.py' 2024-10-17T05:37:21,528 adding 'biocode/ncbigff.py' 2024-10-17T05:37:21,530 adding 'biocode/tbl.py' 2024-10-17T05:37:21,538 adding 'biocode/things.py' 2024-10-17T05:37:21,541 adding 'biocode/utils.py' 2024-10-17T05:37:21,546 adding 'biocode/data/HMPslim.v2.1.obo' 2024-10-17T05:37:21,547 adding 'biocode/data/__init__.py' 2024-10-17T05:37:21,549 adding 'biocode/data/biocode_script_index.json' 2024-10-17T05:37:21,550 adding 'biocode/data/genbank_flat_file_header.template' 2024-10-17T05:37:24,182 adding 'biocode/data/go.obo' 2024-10-17T05:37:25,263 adding 'biocode/data/go.pickle' 2024-10-17T05:37:25,299 adding 'biocode/data/rsem_html_table.template' 2024-10-17T05:37:25,304 adding 'biocode-0.12.0.data/scripts/add_blast_results_to_gff3_product.py' 2024-10-17T05:37:25,305 adding 'biocode-0.12.0.data/scripts/add_gff3_locus_tags.py' 2024-10-17T05:37:25,307 adding 'biocode-0.12.0.data/scripts/add_polypeptide_to_gff3_gene_models.py' 2024-10-17T05:37:25,308 adding 'biocode-0.12.0.data/scripts/append_to_column_9_value.py' 2024-10-17T05:37:25,310 adding 'biocode-0.12.0.data/scripts/append_to_fasta_header.py' 2024-10-17T05:37:25,311 adding 'biocode-0.12.0.data/scripts/append_to_fastq_read_header.py' 2024-10-17T05:37:25,313 adding 'biocode-0.12.0.data/scripts/calculate_gene_coverage_from_assembly.py' 2024-10-17T05:37:25,315 adding 'biocode-0.12.0.data/scripts/calculate_query_coverage_by_blast.py' 2024-10-17T05:37:25,316 adding 'biocode-0.12.0.data/scripts/check_for_embedded_fasta_headers.py' 2024-10-17T05:37:25,318 adding 'biocode-0.12.0.data/scripts/check_gff_for_internal_stops.py' 2024-10-17T05:37:25,320 adding 'biocode-0.12.0.data/scripts/compare_gene_structures.py' 2024-10-17T05:37:25,323 adding 'biocode-0.12.0.data/scripts/convert_aat_btab_to_gff3.py' 2024-10-17T05:37:25,325 adding 'biocode-0.12.0.data/scripts/convert_augustus_to_gff3.py' 2024-10-17T05:37:25,326 adding 'biocode-0.12.0.data/scripts/convert_blast_btab_to_bed.py' 2024-10-17T05:37:25,328 adding 'biocode-0.12.0.data/scripts/convert_blast_btab_to_gff3.py' 2024-10-17T05:37:25,329 adding 'biocode-0.12.0.data/scripts/convert_cegma_gff_to_gff3.py' 2024-10-17T05:37:25,331 adding 'biocode-0.12.0.data/scripts/convert_cufflinks_gtf_to_gff3.py' 2024-10-17T05:37:25,333 adding 'biocode-0.12.0.data/scripts/convert_fasta_contigs_to_gff3.py' 2024-10-17T05:37:25,334 adding 'biocode-0.12.0.data/scripts/convert_fastq_to_fasta.py' 2024-10-17T05:37:25,336 adding 'biocode-0.12.0.data/scripts/convert_genbank_to_gff3.py' 2024-10-17T05:37:25,337 adding 'biocode-0.12.0.data/scripts/convert_gff3_to_bed.py' 2024-10-17T05:37:25,339 adding 'biocode-0.12.0.data/scripts/convert_gff3_to_gbk.py' 2024-10-17T05:37:25,341 adding 'biocode-0.12.0.data/scripts/convert_gff3_to_gene_association_format.py' 2024-10-17T05:37:25,342 adding 'biocode-0.12.0.data/scripts/convert_gff3_to_ncbi_tbl.py' 2024-10-17T05:37:25,343 adding 'biocode-0.12.0.data/scripts/convert_gff_to_ncbi_gff3.py' 2024-10-17T05:37:25,345 adding 'biocode-0.12.0.data/scripts/convert_glimmerHMM_gff_to_gff3.py' 2024-10-17T05:37:25,346 adding 'biocode-0.12.0.data/scripts/convert_htab_to_bed.py' 2024-10-17T05:37:25,348 adding 'biocode-0.12.0.data/scripts/convert_metagenemark_gff_to_gff3.py' 2024-10-17T05:37:25,349 adding 'biocode-0.12.0.data/scripts/convert_pasa_gff_to_models.py' 2024-10-17T05:37:25,351 adding 'biocode-0.12.0.data/scripts/convert_prodigal_to_gff3.py' 2024-10-17T05:37:25,352 adding 'biocode-0.12.0.data/scripts/convert_scipio_gff_to_gff3.py' 2024-10-17T05:37:25,354 adding 'biocode-0.12.0.data/scripts/convert_stringtie_gtf_to_gff3.py' 2024-10-17T05:37:25,356 adding 'biocode-0.12.0.data/scripts/correct_gff3_CDS_phase_column.py' 2024-10-17T05:37:25,357 adding 'biocode-0.12.0.data/scripts/create_rsem_html_table.py' 2024-10-17T05:37:25,359 adding 'biocode-0.12.0.data/scripts/create_taxonomic_profile_from_blast.py' 2024-10-17T05:37:25,361 adding 'biocode-0.12.0.data/scripts/create_taxonomy_db.py' 2024-10-17T05:37:25,362 adding 'biocode-0.12.0.data/scripts/detect_inverted_repeats.py' 2024-10-17T05:37:25,364 adding 'biocode-0.12.0.data/scripts/download_assemblies_from_genbank.py' 2024-10-17T05:37:25,366 adding 'biocode-0.12.0.data/scripts/eggnog_to_sqlite3.py' 2024-10-17T05:37:25,367 adding 'biocode-0.12.0.data/scripts/export_fasta_ids.py' 2024-10-17T05:37:25,369 adding 'biocode-0.12.0.data/scripts/extend_genes_to_stops.py' 2024-10-17T05:37:25,370 adding 'biocode-0.12.0.data/scripts/extract_fasta_regions.py' 2024-10-17T05:37:25,372 adding 'biocode-0.12.0.data/scripts/fasta_base_content.py' 2024-10-17T05:37:25,373 adding 'biocode-0.12.0.data/scripts/fasta_simple_stats.py' 2024-10-17T05:37:25,375 adding 'biocode-0.12.0.data/scripts/fasta_size_distribution_plot.py' 2024-10-17T05:37:25,376 adding 'biocode-0.12.0.data/scripts/fasta_size_report.py' 2024-10-17T05:37:25,378 adding 'biocode-0.12.0.data/scripts/fastq_simple_stats.py' 2024-10-17T05:37:25,379 adding 'biocode-0.12.0.data/scripts/filter_fasta_by_abundance.py' 2024-10-17T05:37:25,380 adding 'biocode-0.12.0.data/scripts/filter_fasta_by_header_regex.py' 2024-10-17T05:37:25,382 adding 'biocode-0.12.0.data/scripts/filter_fasta_by_type.py' 2024-10-17T05:37:25,383 adding 'biocode-0.12.0.data/scripts/filter_fastq_by_N_content.py' 2024-10-17T05:37:25,385 adding 'biocode-0.12.0.data/scripts/filter_gff3_by_id_list.py' 2024-10-17T05:37:25,386 adding 'biocode-0.12.0.data/scripts/filter_uniref_by_repid.py' 2024-10-17T05:37:25,387 adding 'biocode-0.12.0.data/scripts/filter_uniref_by_taxonomy.py' 2024-10-17T05:37:25,389 adding 'biocode-0.12.0.data/scripts/get_mpilup_from_id_list.py' 2024-10-17T05:37:25,391 adding 'biocode-0.12.0.data/scripts/hmmlib_to_sqlite3.py' 2024-10-17T05:37:25,392 adding 'biocode-0.12.0.data/scripts/interleave_fasta.py' 2024-10-17T05:37:25,393 adding 'biocode-0.12.0.data/scripts/interleave_fastq.py' 2024-10-17T05:37:25,395 adding 'biocode-0.12.0.data/scripts/join_columnar_files.py' 2024-10-17T05:37:25,396 adding 'biocode-0.12.0.data/scripts/list_biocode.py' 2024-10-17T05:37:25,397 adding 'biocode-0.12.0.data/scripts/make_cufflinks_ids_unique.py' 2024-10-17T05:37:25,399 adding 'biocode-0.12.0.data/scripts/make_go_index.py' 2024-10-17T05:37:25,401 adding 'biocode-0.12.0.data/scripts/make_go_slim.py' 2024-10-17T05:37:25,403 adding 'biocode-0.12.0.data/scripts/make_go_slim_index.py' 2024-10-17T05:37:25,404 adding 'biocode-0.12.0.data/scripts/mark_partial_genes.py' 2024-10-17T05:37:25,406 adding 'biocode-0.12.0.data/scripts/merge_bam_files.py' 2024-10-17T05:37:25,407 adding 'biocode-0.12.0.data/scripts/merge_fasta_files_and_uniquify_ids.py' 2024-10-17T05:37:25,408 adding 'biocode-0.12.0.data/scripts/merge_masked_fasta_files.py' 2024-10-17T05:37:25,410 adding 'biocode-0.12.0.data/scripts/merge_predicted_gff3.py' 2024-10-17T05:37:25,411 adding 'biocode-0.12.0.data/scripts/prepend_to_fasta_header.py' 2024-10-17T05:37:25,413 adding 'biocode-0.12.0.data/scripts/randomly_subsample_fastq.py' 2024-10-17T05:37:25,414 adding 'biocode-0.12.0.data/scripts/reformat_fasta_residue_lengths.py' 2024-10-17T05:37:25,416 adding 'biocode-0.12.0.data/scripts/remove_duplicate_features.py' 2024-10-17T05:37:25,417 adding 'biocode-0.12.0.data/scripts/remove_duplicate_sequences.py' 2024-10-17T05:37:25,418 adding 'biocode-0.12.0.data/scripts/remove_fasta_from_gff3.py' 2024-10-17T05:37:25,420 adding 'biocode-0.12.0.data/scripts/remove_masked_gene_models.py' 2024-10-17T05:37:25,421 adding 'biocode-0.12.0.data/scripts/remove_orphaned_features.py' 2024-10-17T05:37:25,422 adding 'biocode-0.12.0.data/scripts/reorient_sequences_by_id.py' 2024-10-17T05:37:25,424 adding 'biocode-0.12.0.data/scripts/replace_gff_type_column_value.py' 2024-10-17T05:37:25,425 adding 'biocode-0.12.0.data/scripts/replace_homopolymeric_repeats_with_Ns.py' 2024-10-17T05:37:25,427 adding 'biocode-0.12.0.data/scripts/report_basic_gff_model_agreement.py' 2024-10-17T05:37:25,428 adding 'biocode-0.12.0.data/scripts/report_coverage_gaps.py' 2024-10-17T05:37:25,430 adding 'biocode-0.12.0.data/scripts/report_gff3_statistics.py' 2024-10-17T05:37:25,431 adding 'biocode-0.12.0.data/scripts/report_gff_intron_and_intergenic_stats.py' 2024-10-17T05:37:25,433 adding 'biocode-0.12.0.data/scripts/report_go_slim_counts.py' 2024-10-17T05:37:25,434 adding 'biocode-0.12.0.data/scripts/report_matrix_shape.py' 2024-10-17T05:37:25,436 adding 'biocode-0.12.0.data/scripts/report_or_replace_nonstandard_residues.py' 2024-10-17T05:37:25,438 adding 'biocode-0.12.0.data/scripts/reverse_misordered_cds_coords.py' 2024-10-17T05:37:25,439 adding 'biocode-0.12.0.data/scripts/select_training_and_evaluation_transcripts.py' 2024-10-17T05:37:25,441 adding 'biocode-0.12.0.data/scripts/set_source_column.py' 2024-10-17T05:37:25,442 adding 'biocode-0.12.0.data/scripts/split_fasta_into_even_files.py' 2024-10-17T05:37:25,443 adding 'biocode-0.12.0.data/scripts/split_interleaved_sequence_file.py' 2024-10-17T05:37:25,445 adding 'biocode-0.12.0.data/scripts/split_isoforms_into_individual_genes.py' 2024-10-17T05:37:25,446 adding 'biocode-0.12.0.data/scripts/split_molecules_on_gaps.py' 2024-10-17T05:37:25,448 adding 'biocode-0.12.0.data/scripts/strip_fasta_headers_after_regex.py' 2024-10-17T05:37:25,449 adding 'biocode-0.12.0.data/scripts/subsample_fasta.py' 2024-10-17T05:37:25,451 adding 'biocode-0.12.0.data/scripts/tigrfam_info_to_sqlite3.py' 2024-10-17T05:37:25,452 adding 'biocode-0.12.0.data/scripts/uniprot_sprot_to_sqlite3.py' 2024-10-17T05:37:25,454 adding 'biocode-0.12.0.data/scripts/uniref_to_sqlite3.py' 2024-10-17T05:37:25,456 adding 'biocode-0.12.0.data/scripts/update_selected_column9_values.py' 2024-10-17T05:37:25,458 adding 'biocode-0.12.0.data/scripts/validate_fasta.py' 2024-10-17T05:37:25,459 adding 'biocode-0.12.0.data/scripts/validate_feature_boundaries_on_molecules.py' 2024-10-17T05:37:25,460 adding 'biocode-0.12.0.data/scripts/validate_mate_pairing.py' 2024-10-17T05:37:25,462 adding 'biocode-0.12.0.data/scripts/write_fasta_from_gff.py' 2024-10-17T05:37:25,464 adding 'biocode-0.12.0.dist-info/LICENSE' 2024-10-17T05:37:25,466 adding 'biocode-0.12.0.dist-info/METADATA' 2024-10-17T05:37:25,467 adding 'biocode-0.12.0.dist-info/WHEEL' 2024-10-17T05:37:25,468 adding 'biocode-0.12.0.dist-info/top_level.txt' 2024-10-17T05:37:25,470 adding 'biocode-0.12.0.dist-info/RECORD' 2024-10-17T05:37:25,538 removing build/bdist.linux-armv7l/wheel 2024-10-17T05:37:25,673 Building wheel for biocode (setup.py): finished with status 'done' 2024-10-17T05:37:25,741 Created wheel for biocode: filename=biocode-0.12.0-py3-none-any.whl size=6581784 sha256=93c8e22044533e093628b93bfbe318d80c15d084ab855343f6e103b9604daedd 2024-10-17T05:37:25,742 Stored in directory: /tmp/pip-ephem-wheel-cache-jawrqmu4/wheels/2e/12/5c/0ce3f9a8b55e05f172d01c73b008dc06acb7b4de885a47e5dd 2024-10-17T05:37:25,759 Successfully built biocode 2024-10-17T05:37:25,912 Removed build tracker: '/tmp/pip-build-tracker-23c3sqk5'