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