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    "info": {
        "author": "Kai Blin",
        "author_email": "kblin@biosustain.dtu.dk",
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        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# NCBI Genome Downloading Scripts\n\n[![Build Status](https://github.drone.secondarymetabolites.org/api/badges/kblin/ncbi-genome-download/status.svg)](https://github.drone.secondarymetabolites.org/kblin/ncbi-genome-download)\n[![PyPI release](https://img.shields.io/pypi/v/ncbi-genome-download.svg)](https://pypi.python.org/pypi/ncbi-genome-download/)\n\nSome script to download bacterial and fungal genomes from NCBI after they\nrestructured their FTP a while ago.\n\nIdea shamelessly stolen from [Mick Watson's Kraken downloader\nscripts](http://www.opiniomics.org/building-a-kraken-database-with-new-ftp-structure-and-no-gi-numbers/)\nthat can also be found in [Mick's GitHub\nrepo](https://github.com/mw55309/Kraken_db_install_scripts). However, Mick's\nscripts are ~~written in Perl~~ specific to actually building a Kraken database\n(as advertised).\n\nSo this is a set of scripts that focuses on the actual genome downloading.\n\n## Installation\n\n```\npip install ncbi-genome-download\n```\n\nAlternatively, clone this repository from GitHub, then run (in a python virtual environment)\n```\npip install .\n```\nIf this fails on older versions of Python, try updating your `pip` tool first:\n```\npip install --upgrade pip\n```\nand then rerun the `ncbi-genome-download` install.\n\nAlternatively, `ncbi-genome-download` is packaged in `conda`.\nRefer the the Anaconda/miniconda site to install a distribution (highly recommended) https://conda.io/miniconda.html\nWith that installed one can do:\n```\nconda install -c bioconda ncbi-genome-download\n```\n\n`ncbi-genome-download` is only developed and tested on Python releases still under active\nsupport by the Python project. At the moment, this means versions 2.7, 3.4, 3.5 and 3.6.\nSpecifically, no attempt at testing under Python versions older than 2.7 or 3.4 is being made.\n\nIf your system is stuck on an older version of Python, consider using a tool like\n[Homebrew](http://brew.sh) or [Linuxbrew](http://linuxbrew.sh) to obtain a more up-to-date\nversion.\n\n\n## Usage\n\nTo download all bacterial RefSeq genomes in GenBank format from NCBI, run the following:\n```\nncbi-genome-download bacteria\n```\n\nDownloading multiple groups is also possible:\n```\nncbi-genome-download bacteria,viral\n```\n\n**Note**: To see all available groups, see `ncbi-genome-download --help`, or simply use `all` to check all groups.\nNaming a more specific group will reduce the download size and the time needed to find the sequences to download.\n\nIf you're on a reasonably fast connection, you might want to try running multiple downloads in parallel:\n```\nncbi-genome-download bacteria --parallel 4\n```\n\n\nTo download all fungal GenBank genomes from NCBI in GenBank format, run:\n```\nncbi-genome-download --section genbank fungi\n```\n\nTo download all viral RefSeq genomes in FASTA format, run:\n```\nncbi-genome-download --format fasta viral\n```\n\nIt is possible to download multiple formats by supplying a list of formats or simply download all formats:\n```\nncbi-genome-download --format fasta,assembly-report viral\nncbi-genome-download --format all viral\n```\n\nTo download only completed bacterial RefSeq genomes in GenBank format, run:\n```\nncbi-genome-download --assembly-level complete bacteria\n```\n\nIt is possible to download multiple assembly levels at once by supplying a list:\n```\nncbi-genome-download --assembly-level complete,chromosome bacteria\n```\n\nTo download only bacterial reference genomes from RefSeq in GenBank format, run:\n```\nncbi-genome-download --refseq-category reference bacteria\n```\n\nTo download bacterial RefSeq genomes of the genus _Streptomyces_, run:\n```\nncbi-genome-download --genus Streptomyces bacteria\n```\n**Note**: This is a simple string match on the organism name provided by NCBI only.\n\nYou can also use this with a slight trick to download genomes of a certain species as well:\n```\nncbi-genome-download --genus \"Streptomyces coelicolor\" bacteria\n```\n**Note**: The quotes are important. Again, this is a simple string match on the organism\nname provided by the NCBI.\n\nMultiple genera is also possible:\n```\nncbi-genome-download --genus \"Streptomyces coelicolor,Escherichia coli\" bacteria\n```\n\nYou can also put genus names into a file, one organism per line, e.g.:\n```\nStreptomyces\nAmycolatopsis\n```\n\nThen, pass the path to that file (e.g. `my_genera.txt`) to the `--genus` option, like so:\n```\nncbi-genome-download --genus my_genera.txt bacteria\n```\n**Note**: The above command will download all _Streptomyces_ and _Amycolatopsis_ genomes from RefSeq.\n\nYou can make the string match fuzzy using the `--fuzzy-genus` option. This can be handy if you need to match\na value in the middle of the NCBI organism name, like so:\n\n```\nncbi-genome-download --genus coelicolor --fuzzy-genus bacteria\n```\n**Note**: The above command will download all bacterial genomes containing \"coelicolor\" anywhere in their\norganism name from RefSeq.\n\nTo download bacterial RefSeq genomes based on their NCBI species taxonomy ID, run:\n```\nncbi-genome-download --species-taxid 562 bacteria\n```\n**Note**: The above command will download all RefSeq genomes belonging to _Escherichia coli_.\n\nTo download a specific bacterial RefSeq genomes based on its NCBI taxonomy ID, run:\n```\nncbi-genome-download --taxid 511145 bacteria\n```\n**Note**: The above command will download the RefSeq genome belonging to _Escherichia coli str. K-12 substr. MG1655_.\n\nIt is also possible to download multiple species taxids or taxids by supplying the numbers in a comma-separated list:\n```\nncbi-genome-download --taxid 9606,9685 --assembly-level chromosome vertebrate_mammalian\n```\n**Note**: The above command will download the reference genomes for cat and human.\n\nIn addition, you can put multiple species taxids or taxids into a file, one per line\nand pass that filename to the `--species-taxid` or `--taxid` parameters, respectively.\n\nAssuming you had a file `my_taxids.txt` with the following contents:\n```\n9606\n9685\n```\nYou could download the reference genomes for cat and human like this:\n```\nncbi-genome-download --taxid my_taxids.txt --assembly-level chromosome vertebrate_mammalian\n```\n\nIt is possible to also create a human-readable directory structure in parallel to mirroring\nthe layout used by NCBI:\n```\nncbi-genome-download --human-readable bacteria\n```\nThis will use links to point to the appropriate files in the NCBI directory structure,\nso it saves file space. Note that links are not supported on some Windows file systems and some\nolder versions of Windows.\n\nIt is also possible to re-run a previous download with the `--human-readable` option.\nIn this case, `ncbi-genome-download` will not download any new genome files, and just create\nhuman-readable directory structure. Note that if any files have been changed on the NCBI side,\na file download will be triggered.\n\nThere is a \"dry-run\" option to show which accessions would be downloaded, given your filters:\n```\nncbi-genome-download --dry-run bacteria\n```\n\nIf you want to filter for the \"relation to type material\" column of the\nassembly summary file, you can use the `--type-material` option. Possible\nvalues are \"any\", \"all\", \"type\", \"reference\", \"synonym\", \"proxytype\", and/or\n\"neotype\". \"any\" will include assemblies with no relation to type material\nvalue defined, \"all\" will download only assemblies with a defined value.\nMultiple values can be given, separated by comma:\n```\nncbi-genome-download --type-material type,reference\n```\n\nBy default, ncbi-genome-download caches the assembly summary files for the respective taxonomic\ngroups for one day. You can skip using the cache file by using the `--no-cache` option.\nThe output of `--help` also shows the cache directory, should you want to remove any of the cached\nfiles.\n\nTo get an overview of all options, run\n```\nncbi-genome-download --help\n```\n\n### As a method\nYou can also use it as a method call. Pass the pythonised keyword arguments (`_` instead of `-`)\n as described above or in the `--help`:\n```\nimport ncbi_genome_download as ngd\nngd.download()\n```\n**Note**: To specify a taxonomic group, like *bacteria*, use the `group` keyword.\n\n\n### Contributed Scripts: `gimme_taxa.py`\nThis script lets you find out what TaxIDs to pass to `ngd`, and will write a simple one-item-per-line\nfile to pass in to it. It utilises the `ete3` toolkit, so refer to their site to install the dependency\nif it's not already satisfied.\n\nYou can query the database using a particular TaxID, or a scientific name. The primary function of the\nscript is to return all the child taxa of the specified parent taxa. The script has various options\nfor what information is written in the output.\n\nA basic invocation may look like:\n\n```\n# Fetch all descendent taxa for Escherichia (taxid 561):\npython gimme_taxa.py -o ~/mytaxafile.txt 561\n\n# Alternatively, just provide the taxon name\npython gimme_taxa.py -o all_descendent_taxids.txt Escherichia\n\n# You can provide multiple taxids and/or names\npython gimme_taxa.py -o all_descendent_taxids.txt 561,Methanobrevibacter\n```\n\nOn first use, a small sqlite database will be created in your home directory\nby default (change the location with the `--database` flag). You can update this database\nby using the `--update` flag. Note that if the database is not in your home directory,\nyou must specify it with `--database` or a new database will be created in your home\ndirectory.\n\nTo see all help:\n```\npython gimme_taxa.py\npython gimme_taxa.py -h\npython gimme_taxa.py --help\n```\n\n## License\nAll code is available under the Apache License version 2, see the\n[`LICENSE`](LICENSE) file for details.\n\n\n",
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