https://github.com/biomadeira/biodownloader

📦 A Command Line Tool for downloading protein structures, sequences and MSAs
https://github.com/biomadeira/biodownloader

bioinformatics cath cli fasta gff mmcif pdb pfam sifts

Last synced: 3 months ago
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📦 A Command Line Tool for downloading protein structures, sequences and MSAs

• Host: GitHub
• URL: https://github.com/biomadeira/biodownloader
• Owner: biomadeira
• License: gpl-3.0
• Created: 2017-06-23T23:16:51.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-11-21T11:50:58.000Z (almost 8 years ago)
• Last Synced: 2023-10-20T18:16:34.625Z (about 2 years ago)
• Topics: bioinformatics, cath, cli, fasta, gff, mmcif, pdb, pfam, sifts
• Language: Python
• Homepage:
• Size: 47.9 KB
• Stars: 9
• Watchers: 2
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.md

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README

          
BioDownloader

=============

|Build Status| |Coverage Status| |Health| |Python: versions| |License|

A Command Line Tool for downloading protein structures, protein sequences

and multiple sequence alignments.

Setup

~~~~~

Easy install from github using pip.

.. code:: bash

    $ pip install --upgrade http://github.com/biomadeira/BioDownloader/zipball/master

If you want to mess up with the source code.

.. code:: bash

    $ git clone https://github.com/biomadeira/BioDownloader.git

    $ cd BioDownloader

    $ sudo python setup.py install

Quickstart

~~~~~~~~~~

Printing help information...

::

   $ BioDownloader -h

   Usage: BioDownloader [OPTIONS] COMMAND1 [ARGS]... [COMMAND2 [ARGS]...]...

     BioDownloader: a Command Line Tool for downloading protein structures,

     protein sequences and multiple sequence alignments.

         $ BioDownloader COMMAND --help for additional help

   Options:

     --version      Show the version and exit.

     -h, --help     Show this message and exit.

   Commands:

     cath     Multiple sequence alignments (fasta) from...

     pdb      Macromolecular structures from the PDBe.

     pfam     Multiple sequence alignments (fasta) from...

     sifts    SIFTS xml structure-sequence mappings from...

     uniprot  Sequences (fasta) and sequence annotations in...

Printing help information for one of the available commands...

::

   $ BioDownloader uniprot -h

   Usage: BioDownloader uniprot [OPTIONS] IDS...

     Sequences (fasta) and sequence annotations in SwissProt (txt) or GFF (gff)

     format from the UniProt.

     Pass one or more accession IDs (e.g. 'P00439' or 'P00439 P12345').

   Options:

     --fasta        UniProt sequence in fasta format (expects UniProt ID).

     --gff          UniProt record in gff format (expects UniProt ID).

     --txt          UniProt record in txt format (expects UniProt ID).

     -v, --verbosity LVL  Either CRITICAL, ERROR, WARNING, INFO or DEBUG

     --override     Overrides any existing file, if available.

     --output TEXT  Directory path to which the files will be written.

     -h, --help     Show this message and exit.

Downloading a bunch of structure files...

.. code:: bash

    # Downloads structures in PDB and mmCIF format

    $ BioDownloader pdb --pdb --mmcif 2pah 3pah 4pah

Changing where the files will be downloaded to...

.. code:: bash

    # Downloads a UniProt sequence in FASTA and sequence annotations in GFF

    $ BioDownloader uniprot --fasta --gff --output /path/to/output/dir/ P00439

Dependencies

~~~~~~~~~~~~

See the necessary `requirements`_ for this module.

Contributing and Bug tracking

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Feel free to fork, clone, share and distribute. If you find any bugs or

issues please log them in the `issue tracker`_.

Contributors

~~~~~~~~~~~~

 - `Fábio Madeira`_

 - `Felix Simkovic`_

License

~~~~~~~

GNU General Public License v3 (GPLv3). See `license`_ for details.

.. _requirements: https://github.com/biomadeira/BioDownloader/blob/master/requirements.txt

.. _issue tracker: https://github.com/biomadeira/BioDownloader/issues

.. _license: https://github.com/biomadeira/BioDownloader/blob/master/LICENSE.md

.. _Fábio Madeira: https://github.com/biomadeira

.. _Felix Simkovic: https://github.com/fsimkovic

.. |Build Status| image:: https://secure.travis-ci.org/biomadeira/BioDownloader.png?branch=master

   :target: http://travis-ci.org/biomadeira/BioDownloader

.. |Coverage Status| image:: https://coveralls.io/repos/github/biomadeira/BioDownloader/badge.svg?branch=master

   :target: https://coveralls.io/github/biomadeira/BioDownloader?branch=master

.. |License| image:: http://img.shields.io/badge/license-GPLv3-brightgreen.svg?style=flat

   :target: https://github.com/biomadeira/BioDownloader/blob/master/LICENSE.md

.. |Python: versions| image:: https://img.shields.io/badge/python-3.4,_3.5,_3.6-blue.svg?style=flat

   :target: http://travis-ci.org/biomadeira/BioDownloader

.. |Health| image:: https://landscape.io/github/biomadeira/BioDownloader/master/landscape.svg?style=flat

   :target: https://landscape.io/github/biomadeira/BioDownloader/master