{ "info": { "author": "Simon van Heeringen", "author_email": "simon.vanheeringen@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: MacOS :: MacOS X", "Operating System :: POSIX :: Linux", "Programming Language :: Python", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "genomepy\n========\n\n|bioconda-badge| |PyPI version| |Build Status| |Code Health|\n\n|status| |DOI|\n\nEasily install and use genomes in Python and elsewhere!\n\nThe goal is to have a *simple* and *straightforward* way to download and\nuse genomic sequences. Currently, genomepy supports UCSC, Ensembl and\nNCBI.\n\n|asciicast|\n\n**Pssst, hey there!** Is genomepy not doing what you want? Does it fail?\nIs it clunky? Is the documentation unclear? Have any other ideas on how\nto improve it? Don\u2019t be shy and `let us\nknow `__!\n\nInstallation\n------------\n\nGenomepy works with Python 3.4+. You can install it via\n`bioconda `__:\n\n::\n\n $ conda install genomepy\n\nOr via pip:\n\n::\n\n $ pip install genomepy\n\nIf you install via pip, you will have to install some dependencies, only\nif you want to use the annotation download feature. You will have to\ninstall the following utilities and make sure they are in your PATH:\n\n- ``genePredToBed``\n- ``genePredToGtf``\n- ``bedToGenePred``\n- ``gtfToGenePred``\n- ``gff3ToGenePred``\n\nYou can find the binaries\n`here `__.\n\nPlugins and indexing\n--------------------\n\nBy default ``genomepy`` generates a file with chromosome sizes and a BED\nfile with gap locations (Ns in the sequence).\n\nFor some genomes genomepy can download blacklist files (generated by the\nKundaje lab). This will only work when installing these genomes from\nUCSC. Enable this plugin to use it.\n\n::\n\n $ genomepy plugin enable blacklist\n\nYou can also create indices for some widely using aligners. Currently,\ngenomepy supports:\n\n- `bowtie2 `__\n- `bwa `__\n- `gmap `__\n- `hisat2 `__\n- `minimap2 `__\n\nNote 1: these programs are not installed by genomepy and need to be\ninstalled seperately for the indexing to work.\n\nNote 2: the index is based on the genome, annotation (splice sites) is\ncurrently not taken into account.\n\nYou can configure the index creation using the ``genomepy plugin``\ncommand (see below)\n\nConfiguration\n-------------\n\nTo change the default configuration, generate a personal config file:\n\n::\n\n $ genomepy config generate\n Created config file /home/simon/.config/genomepy/genomepy.yaml\n\nGenome location\n~~~~~~~~~~~~~~~\n\nBy default genomes will be saved in ``~/.local/share/genomes``.\n\nTo set the default genome directory to ``/data/genomes`` for instance,\nedit ``~/.config/genomepy/genomepy.yaml`` and change the following line:\n\n::\n\n genome_dir: ~/.local/share/genomes/\n\nto:\n\n::\n\n genome_dir: /data/genomes\n\nThe genome directory can also be explicitly specified in both the Python\nAPI as well as on the command-line.\n\nCompression\n~~~~~~~~~~~\n\nOptionally genome FASTA files can be saved using bgzip compression. This\nmeans that the FASTA files will take up less space on disk. To enable\nthis, add the following line to your config file:\n\n::\n\n bgzip: True\n\nMost tools are able to use bgzip-compressed genome files. One notable\nexception is ``bedtools getfasta``. As an alternative, you can use the\n``faidx`` command-line script from\n`pyfaidx `__ which comes installed\nwith genomepy.\n\nUsage\n-----\n\nCommand line\n~~~~~~~~~~~~\n\n::\n\n Usage: genomepy [OPTIONS] COMMAND [ARGS]...\n\n Options:\n --version Show the version and exit.\n -h, --help Show this message and exit.\n\n Commands:\n config manage configuration\n genomes list available genomes\n install install genome\n plugin manage plugins\n providers list available providers\n search search for genomes\n\nInstall a genome.\n^^^^^^^^^^^^^^^^^\n\nThe most important command. The most simple form:\n\n::\n\n $ genomepy install hg38 UCSC \n downloading...\n done...\n name: hg38\n fasta: /data/genomes/hg38/hg38.fa\n\nHere, genomes are downloaded to the directory specified in the config\nfile. To choose a different directory, use the ``-g`` option.\n\n::\n\n $ genomepy install sacCer3 UCSC -g ~/genomes/\n downloading from http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz...\n done...\n name: sacCer3\n local name: sacCer3\n fasta: /home/simon/genomes/sacCer3/sacCer3.fa\n\nYou can use a regular expression to filter for matching sequences (or\nnon-matching sequences by using the ``--no-match`` option). For\ninstance, the following command downloads hg38 and saves only the major\nchromosomes:\n\n::\n\n $ genomepy install hg38 UCSC -r 'chr[0-9XY]+$'\n downloading from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz...\n done...\n name: hg38\n local name: hg38\n fasta: /data/genomes/hg38/hg38.fa\n $ grep \">\" /data/genomes/hg38/hg38.fa\n >chr1\n >chr10\n >chr11\n >chr12\n >chr13\n >chr14\n >chr15\n >chr16\n >chr17\n >chr18\n >chr19\n >chr2\n >chr20\n >chr21\n >chr22\n >chr3\n >chr4\n >chr5\n >chr6\n >chr7\n >chr8\n >chr9\n >chrX\n >chrY\n\nBy default, sequences are soft-masked. Use ``-m hard`` for hard masking.\n\nThe chromosome sizes are saved in file called\n``.fa.sizes``.\n\nFor genomes from UCSC and Ensembl, you can choose to download gene\nannotation files with the ``--annotation`` option. These will be saved\nin BED and GTF format.\n\n::\n\n $ genomepy install hg38 UCSC --annotation\n\nFinally, in the spirit of reproducibility all selected options are\nstored in a ``README.txt``. This includes the original name and download\nlocation.\n\nManage plugins.\n^^^^^^^^^^^^^^^\n\nUse ``genomepy plugin list`` to view the available plugins.\n\n::\n\n $ genomepy plugin list\n plugin enabled\n bowtie2 \n bwa \n gaps *\n gmap \n hisat2 \n minimap2 \n sizes *\n\nEnable plugins as follows:\n\n::\n\n $ genomepy plugin enable bwa hisat2\n Enabled plugins: bwa, gaps, hisat2, sizes\n\nAnd disable like this:\n\n::\n\n $ genomepy plugin disable bwa\n Enabled plugins: gaps, hisat2, sizes\n\nSearch for a genome.\n^^^^^^^^^^^^^^^^^^^^\n\n::\n\n $ genomepy search Xenopus\n NCBI Xenopus_tropicalis_v9.1 Xenopus tropicalis; DOE Joint Genome Institute\n NCBI ViralProj30173 Xenopus laevis endogenous retrovirus Xen1; \n NCBI Xenopus_laevis_v2 Xenopus laevis; International Xenopus Sequencing Consortium\n NCBI v4.2 Xenopus tropicalis; DOE Joint Genome Institute\n NCBI Xtropicalis_v7 Xenopus tropicalis; DOE Joint Genome Institute\n Ensembl JGI 4.2 Xenopus\n\nOnly search a specific provider:\n\n::\n\n $ genomepy search tropicalis -p UCSC\n UCSC xenTro7 X. tropicalis Sep. 2012 (JGI 7.0/xenTro7) Genome at UCSC\n UCSC xenTro3 X. tropicalis Nov. 2009 (JGI 4.2/xenTro3) Genome at UCSC\n UCSC xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) Genome at UCSC\n UCSC xenTro1 X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) Genome at UCSC\n\nNote that searching doesn\u2019t work flawlessly, so try a few variations if\nyou don\u2019t get any results. Search is case-insensitive.\n\nList available providers\n^^^^^^^^^^^^^^^^^^^^^^^^\n\n::\n\n $ genomepy providers\n Ensembl\n UCSC\n NCBI\n\nList available genomes\n^^^^^^^^^^^^^^^^^^^^^^\n\nYou can constrain the genome list by using the ``-p`` option to search\nonly a specific provider.\n\n::\n\n $ genomepy genomes -p UCSC\n UCSC hg38 Human Dec. 2013 (GRCh38/hg38) Genome at UCSC\n UCSC hg19 Human Feb. 2009 (GRCh37/hg19) Genome at UCSC\n UCSC hg18 Human Mar. 2006 (NCBI36/hg18) Genome at UCSC\n ...\n UCSC danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) Genome at UCSC\n UCSC danRer3 Zebrafish May 2005 (Zv5/danRer3) Genome at UCSC\n\nManage configuration\n^^^^^^^^^^^^^^^^^^^^\n\nList the current configuration file that genomepy uses:\n\n::\n\n $ genomepy config file\n /home/simon/.config/genomepy/genomepy.yaml\n\nTo show the contents of the config file:\n\n::\n\n $ genomepy config show\n # Directory were downloaded genomes will be stored\n genome_dir: ~/.local/share/genomes/\n\n plugin:\n - gaps\n - sizes\n\nTo generate a personal configuration file (existing file will be\noverwritten):\n\n::\n\n $ genomepy config generate\n Created config file /home/simon/.config/genomepy/genomepy.yaml\n\nLocal cache.\n^^^^^^^^^^^^\n\nNote that the first time you run ``genomepy search`` or ``list`` the\ncommand will take a long time as the genome lists have to be downloaded.\nThe lists are cached locally, which will save time later. The cached\nfiles are stored in ``~/.cache/genomepy`` and expire after 7 days. You\ncan also delete this directory to clean the cache.\n\nFrom Python\n~~~~~~~~~~~\n\n.. code:: python\n\n >>> import genomepy\n >>> for row in genomepy.search(\"GRCh38\"):\n ... print(\"\\t\".join(row))\n ...\n UCSC hg38 Human Dec. 2013 (GRCh38/hg38) Genome at UCSC\n NCBI GRCh38.p10 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p1 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p2 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p3 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p4 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p5 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p6 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p7 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p8 Homo sapiens; Genome Reference Consortium\n NCBI GRCh38.p9 Homo sapiens; Genome Reference Consortium\n Ensembl GRCh38.p10 Human\n >>> genomepy.install_genome(\"hg38\", \"UCSC\", genome_dir=\"/data/genomes\")\n downloading...\n done...\n name: hg38\n fasta: /data/genomes/hg38/hg38.fa\n >>> g = genomepy.Genome(\"hg38\", genome_dir=\"/data/genomes\")\n >>> g[\"chr6\"][166502000:166503000]\n tgtatggtccctagaggggccagagtcacagagatggaaagtggatggcgggtgccgggggctggggagctactgtgcagggggacagagctttagttctgcaagatgaaacagttctggagatggacggtggggatgggggcccagcaatgggaacgtgcttaatgccactgaactgggcacttaaacgtggtgaaaactgtaaaagtcatgtgtatttttctacaattaaaaaaaATCTGCCACAGAGTTAAAAAAATAACCACTATTTTCTGGAAATGGGAAGGAAAAGTTACAGCATGTAATTAAGATGACAATTTATAATGAACAAGGCAAATCTTTTCATCTTTGCCTTTTGGGCATATTCAATCTTTGCCCAGAATTAAGCACCTTTCAAGATTAATTCTCTAATAATTCTAGTTGAACAACACAACCTTTTCCTTCAAGCTTGCAATTAAATAAGGCTATTTTTAGCTGTAAGGATCACGCTGACCTTCAGGAGCAATGAGAACCGGCACTCCCGGCCTGAGTGGATGCACGGGGAGTGTGTCTAACACACAGGCGTCAACAGCCAGGGCCGCACGAGGAGGAGGAGTGGCAACGTCCACACAGACTCACAACACGGCACTCCGACTTGGAGGGTAATTAATACCAGGTTAACTTCTGGGATGACCTTGGCAACGACCCAAGGTGACAGGCCAGGCTCTGCAATCACCTCCCAATTAAGGAGAGGCGAAAGGGGACTCCCAGGGCTCAGAGCACCACGGGGTTCTAGGTCAGACCCACTTTGAAATGGAAATCTGGCCTTGTGCTGCTGCTCTTGTGGGGAGACAGCAGCTGCGGAGGCTGCTCTCTTCATGGGATTACTCTGGATAAAGTCTTTTTTGATTCTACgttgagcatcccttatctgaaatgcctgaaaccggaagtgtttaggatttggggattttgcaatatttacttatatataatgagatatcttggagatgggccacaa\n\nThe ``genomepy.Genome()`` method returns a Genome object. This has all\nthe functionality of a ``pyfaidx.Fasta`` object, see the\n`documentation `__ for more examples\non how to use this.\n\nKnown issues\n------------\n\nThere might be issues with specific genome sequences. Sadly, not\neverything (naming, structure, filenames) is always consistent on the\nprovider end. Let me know if you encounter issues with certain\ndownloads.\n\nTodo\n----\n\n- Linking genomes to NCBI taxonomy ID\n- Optionally: Ensembl bacteria (although there might be better options\n specifically for bacterial sequences)\n\nCitation\n--------\n\nIf you use genomepy in your research, please cite it:\n`10.21105/joss.00320 `__.\n\nGetting help\n------------\n\nIf you want to report a bug or issue, or have problems with installing\nor running the software please create `a new\nissue `__. This is the\npreferred way of getting support. Alternatively, you can `mail\nme `__.\n\nContributing\n------------\n\nContributions welcome! Send me a pull request or get in\n`touch `__.\n\nLicense\n-------\n\nThis module is licensed under the terms of the `MIT\nlicense `__.\n\n.. |bioconda-badge| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat\n :target: http://bioconda.github.io\n.. |PyPI version| image:: https://badge.fury.io/py/genomepy.svg\n :target: https://badge.fury.io/py/genomepy\n.. |Build Status| image:: https://travis-ci.org/simonvh/genomepy.svg?branch=master\n :target: https://travis-ci.org/simonvh/genomepy\n.. |Code Health| image:: https://landscape.io/github/simonvh/genomepy/master/landscape.svg?style=flat\n :target: https://landscape.io/github/simonvh/genomepy/master\n.. |status| image:: http://joss.theoj.org/papers/df434a15edd00c8c2f4076668575d1cd/status.svg\n :target: http://joss.theoj.org/papers/df434a15edd00c8c2f4076668575d1cd\n.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.831969.svg\n :target: https://doi.org/10.5281/zenodo.831969\n.. |asciicast| 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