{"id":29508500,"url":"https://github.com/biomadeira/biodownloader","last_synced_at":"2025-07-16T05:15:29.422Z","repository":{"id":144770496,"uuid":"95262925","full_name":"biomadeira/BioDownloader","owner":"biomadeira","description":"📦 A Command Line Tool for downloading protein structures, sequences and MSAs","archived":false,"fork":false,"pushed_at":"2017-11-21T11:50:58.000Z","size":49,"stargazers_count":9,"open_issues_count":3,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-10-20T18:16:34.625Z","etag":null,"topics":["bioinformatics","cath","cli","fasta","gff","mmcif","pdb","pfam","sifts"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biomadeira.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-06-23T23:16:51.000Z","updated_at":"2023-10-20T18:16:35.183Z","dependencies_parsed_at":"2023-10-20T18:26:39.825Z","dependency_job_id":null,"html_url":"https://github.com/biomadeira/BioDownloader","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"purl":"pkg:github/biomadeira/BioDownloader","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomadeira%2FBioDownloader","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomadeira%2FBioDownloader/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomadeira%2FBioDownloader/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomadeira%2FBioDownloader/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biomadeira","download_url":"https://codeload.github.com/biomadeira/BioDownloader/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomadeira%2FBioDownloader/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265483900,"owners_count":23774291,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","cath","cli","fasta","gff","mmcif","pdb","pfam","sifts"],"created_at":"2025-07-16T05:15:28.768Z","updated_at":"2025-07-16T05:15:29.408Z","avatar_url":"https://github.com/biomadeira.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"BioDownloader\n=============\n\n|Build Status| |Coverage Status| |Health| |Python: versions| |License|\n\nA Command Line Tool for downloading protein structures, protein sequences\nand multiple sequence alignments.\n\nSetup\n~~~~~\n\nEasy install from github using pip.\n\n.. code:: bash\n\n    $ pip install --upgrade http://github.com/biomadeira/BioDownloader/zipball/master\n\n\n\nIf you want to mess up with the source code.\n\n.. code:: bash\n\n    $ git clone https://github.com/biomadeira/BioDownloader.git\n    $ cd BioDownloader\n    $ sudo python setup.py install\n\n\n\nQuickstart\n~~~~~~~~~~\n\nPrinting help information...\n\n::\n\n   $ BioDownloader -h\n   Usage: BioDownloader [OPTIONS] COMMAND1 [ARGS]... [COMMAND2 [ARGS]...]...\n\n     BioDownloader: a Command Line Tool for downloading protein structures,\n     protein sequences and multiple sequence alignments.\n\n         $ BioDownloader COMMAND --help for additional help\n\n   Options:\n     --version      Show the version and exit.\n     -h, --help     Show this message and exit.\n\n   Commands:\n     cath     Multiple sequence alignments (fasta) from...\n     pdb      Macromolecular structures from the PDBe.\n     pfam     Multiple sequence alignments (fasta) from...\n     sifts    SIFTS xml structure-sequence mappings from...\n     uniprot  Sequences (fasta) and sequence annotations in...\n\n\nPrinting help information for one of the available commands...\n\n::\n\n   $ BioDownloader uniprot -h\n   Usage: BioDownloader uniprot [OPTIONS] IDS...\n\n     Sequences (fasta) and sequence annotations in SwissProt (txt) or GFF (gff)\n     format from the UniProt.\n\n     Pass one or more accession IDs (e.g. 'P00439' or 'P00439 P12345').\n\n   Options:\n     --fasta        UniProt sequence in fasta format (expects UniProt ID).\n     --gff          UniProt record in gff format (expects UniProt ID).\n     --txt          UniProt record in txt format (expects UniProt ID).\n     -v, --verbosity LVL  Either CRITICAL, ERROR, WARNING, INFO or DEBUG\n     --override     Overrides any existing file, if available.\n     --output TEXT  Directory path to which the files will be written.\n     -h, --help     Show this message and exit.\n\n\nDownloading a bunch of structure files...\n\n.. code:: bash\n\n    # Downloads structures in PDB and mmCIF format\n    $ BioDownloader pdb --pdb --mmcif 2pah 3pah 4pah\n\n\nChanging where the files will be downloaded to...\n\n.. code:: bash\n\n    # Downloads a UniProt sequence in FASTA and sequence annotations in GFF\n    $ BioDownloader uniprot --fasta --gff --output /path/to/output/dir/ P00439\n\n\n\nDependencies\n~~~~~~~~~~~~\n\nSee the necessary `requirements`_ for this module.\n\nContributing and Bug tracking\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nFeel free to fork, clone, share and distribute. If you find any bugs or\nissues please log them in the `issue tracker`_.\n\n\nContributors\n~~~~~~~~~~~~\n\n - `Fábio Madeira`_\n - `Felix Simkovic`_\n\n\nLicense\n~~~~~~~\n\nGNU General Public License v3 (GPLv3). See `license`_ for details.\n\n.. _requirements: https://github.com/biomadeira/BioDownloader/blob/master/requirements.txt\n.. _issue tracker: https://github.com/biomadeira/BioDownloader/issues\n.. _license: https://github.com/biomadeira/BioDownloader/blob/master/LICENSE.md\n.. _Fábio Madeira: https://github.com/biomadeira\n.. _Felix Simkovic: https://github.com/fsimkovic\n\n.. |Build Status| image:: https://secure.travis-ci.org/biomadeira/BioDownloader.png?branch=master\n   :target: http://travis-ci.org/biomadeira/BioDownloader\n.. |Coverage Status| image:: https://coveralls.io/repos/github/biomadeira/BioDownloader/badge.svg?branch=master\n   :target: https://coveralls.io/github/biomadeira/BioDownloader?branch=master\n.. |License| image:: http://img.shields.io/badge/license-GPLv3-brightgreen.svg?style=flat\n   :target: https://github.com/biomadeira/BioDownloader/blob/master/LICENSE.md\n.. |Python: versions| image:: https://img.shields.io/badge/python-3.4,_3.5,_3.6-blue.svg?style=flat\n   :target: http://travis-ci.org/biomadeira/BioDownloader\n.. |Health| image:: https://landscape.io/github/biomadeira/BioDownloader/master/landscape.svg?style=flat\n   :target: https://landscape.io/github/biomadeira/BioDownloader/master\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiomadeira%2Fbiodownloader","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiomadeira%2Fbiodownloader","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiomadeira%2Fbiodownloader/lists"}