{
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        "author": "F\u00e1bio Madeira",
        "author_email": "tbrittoborges@dundee.ac.uk",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: Implementation :: PyPy",
            "Topic :: Internet",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules"
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        "description": "ProteoFAV\n=========\n\n**Protein Feature Aggregation and Variants**\n\n|Pypi| |Build Status| |Documentation| |Python: versions| |License|\n\n.. |Pypi| image:: https://img.shields.io/pypi/v/proteofav.svg\n  :target: https://pypi.python.org/pypi/proteofav\n.. |Build Status| image:: https://img.shields.io/travis/bartongroup/proteofav.svg\n  :target: https://travis-ci.org/bartongroup/proteofav\n.. |Documentation| image:: https://readthedocs.org/projects/proteofav/badge/?version=latest\n  :target: https://proteofav.readthedocs.io/en/latest/?badge=latest\n  :alt: Documentation Status\n.. |Coverage Status| image:: https://coveralls.io/repos/github/bartongroup/proteofav/badge.svg?branch=master\n  :target: https://coveralls.io/github/bartongroup/proteofav?branch=master\n.. |Health| image:: https://landscape.io/github/bartongroup/proteofav/master/landscape.svg?style=flat\n  :target: https://landscape.io/github/bartongroup/proteofav/master\n.. |Pyup| image:: https://pyup.io/repos/github/bartongroup/proteofav/shield.svg\n   :target: https://pyup.io/repos/github/bartongroup/proteofav/\n   :alt: Updates\n.. |License| image:: http://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat\n  :target: https://github.com/bartongroup/proteofav//blob/master/LICENSE.md\n.. |Python: versions| image:: https://img.shields.io/badge/python-3.5,_3.6-blue.svg?style=flat\n   :target: http://travis-ci.org/bartongroup/proteofav/\n\nProteoFAV is a Python module that address the challenge of cross-mapping protein structures and protein sequences,\nallowing for protein structures to be annotated with sequence features. It implements methods for working with\nprotein structures (via mmCIF, PDB, PDB Validation, DSSP and SIFTS files), sequence Features (via UniProt GFF annotations) and\ngenetic variants (via UniProt/EBI Proteins API and Ensembl REST API). Cross-mapping of structure and sequence is\nperformed with the aid of SIFTS.\n\nProteFAV relies heavily in the `Pandas`_ library to quickly load data into DataFrames for fast\ndata exploration and analysis. Structure and sequence\ndata are parsed/fetched onto Pandas DataFrames that are then merged-together (collapsed) onto a\nsingle DataFrame.\n\nGetting Started\n---------------\n\nDependencies\n~~~~~~~~~~~~\n\nProteoFAV was developed to support Python 3.5+ and Pandas 0.20+.\n\nCheck `requirements`_ for specific requirements.\n\n.. _requirements: https://github.com/bartongroup/ProteoFAV/blob/master/requirements.txt\n\n\nInstallation\n~~~~~~~~~~~~\n\nTo install the stable release, run this command in your terminal:\n\n.. code-block:: console\n\n    $ pip install proteofav\n\nIf you don't have `pip`_ installed, this `Python installation guide`_ can guide\nyou through the process.\n\n.. _pip: https://pip.pypa.io\n.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/\n\n\nInstalling from source in a virtual environment\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nGetting ProteoFAV:\n\n.. code-block:: bash\n\n    $ wget https://github.com/bartongroup/ProteoFAV/archive/master.zip -O ProteoFAV.zip\n    $ unzip ProteoFAV.zip\n\n    # alternatively, cloning the git repository\n    $ git clone https://github.com/bartongroup/ProteoFAV.git\n\n\nInstalling With Conda:\n\n.. code-block:: bash\n\n    $ conda-env create -n proteofav -f path/to/ProteoFAV/requirements.txt\n    $ source activate proteofav\n    $ cd path/to/ProteoFAV\n    $ pip install .\n\nInstalling with Virtualenv:\n\n.. code-block:: bash\n\n    $ virtualenv --python `which python` env\n    $ source env/bin/activate\n    $ pip install -r requirements.txt\n    $ python path/to/ProteoFAV/setup.py install\n\n\nTesting the installation\n~~~~~~~~~~~~~~~~~~~~~~~~\n\nTest dependencies should be resolved with:\n\n.. code-block:: bash\n\n    $ python path/to/ProteoFAV/setup.py develop --user\n\n\nRun the Tests with:\n\n.. code-block:: bash\n\n    $ python path/to/ProteoFAV/setup.py test\n    # or\n    $ cd path/to/ProteoFAV/tests\n    $ python -m unittest discover\n\n\nProteoFAV Configuration\n~~~~~~~~~~~~~~~~~~~~~~~\n\nProteoFAV uses a configuration file `config.ini` where the user can specify the directory paths, as well as urls for commonly used data sources.\n\nAfter installing run:\n\n.. code-block:: bash\n\n    $ proteofav-setup\n\n\nExample Usage\n-------------\n\nExample usage is currently provided as a `Jupyter Notebook`, which can be viewed with the `GitHub's`_ file viewer or with the Jupyter `nbviewer`_.\n\nYou can download the Jupyter notebook from `GitHub`_ and test it with your ProteoFAV's installation.\n\n.. _GitHub's: https://github.com/bartongroup/ProteoFAV/blob/master/Examples.ipynb\n.. _nbviewer: https://nbviewer.jupyter.org/github/bartongroup/ProteoFAV/blob/master/Examples.ipynb\n.. _GitHub: https://github.com/bartongroup/ProteoFAV\n\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\nBefore you submit your *Pull-requests* read the `Contributing Guide`_.\n\nCredits\n-------\n\nSee the `Credits`_\n\n\nChangelog\n---------\n\nSee the `Changelog`_\n\n\nLicensing\n---------\n\nThe MIT License (MIT). See `license`_ for details.\n\n.. _requirements: https://github.com/bartongroup/ProteoFAV/blob/master/requirements.txt\n.. _license: https://github.com/bartongroup/ProteoFAV/blob/master/LICENSE.md\n.. _issue tracker: https://github.com/bartongroup/ProteoFAV/issues\n.. _docs: https://github.com/bartongroup/ProteoFAV/blob/master/docs/index.rst\n.. _Pandas: http://pandas.pydata.org/\n.. _Contributing Guide: https://github.com/bartongroup/ProteoFAV/wiki/Contributing-Guide\n.. _Changelog: https://github.com/bartongroup/ProteoFAV/blob/master/CHANGELOG.rst\n.. _Credits: https://github.com/bartongroup/ProteoFAV/blob/master/AUTHORS.rst\n",
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