Metadata-Version: 1.1
Name: ndexbiogridloader
Version: 0.1.2
Summary: Loads BioGRID data into NDEx
Home-page: https://github.com/ndexcontent/ndexbiogridloader
Author: Vladimir Rynkov
Author-email: vrynkov@ucsd.edu
License: BSD license
Description: ===========================
        NDEx BioGRID Content Loader
        ===========================
        
        
        .. image:: https://img.shields.io/pypi/v/ndexbiogridloader.svg
                :target: https://pypi.python.org/pypi/ndexbiogridloader
        
        .. image:: https://img.shields.io/travis/ndexcontent/ndexbiogridloader.svg
                :target: https://travis-ci.org/ndexcontent/ndexbiogridloader
        
        .. image:: https://coveralls.io/repos/github/ndexcontent/ndexbiogridloader/badge.svg?branch=master
                :target: https://coveralls.io/github/ndexcontent/ndexbiogridloader?branch=master
        
        .. image:: https://readthedocs.org/projects/ndexbiogridloader/badge/?version=latest
                :target: https://ndexbiogridloader.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        Python application for loading BioGRID data into `NDEx <http://ndexbio.org>`_.
        
        This tool downloads and unpacks the `BioGRID <https://thebiogrid.org/>`_ files below
        
            `BIOGRID-ORGANISM-3.5.175.tab2.zip <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.175/BIOGRID-ORGANISM-3.5.175.tab2.zip>`_
        
            `BIOGRID-CHEMICALS-3.5.175.chemtab.zip <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.175/BIOGRID-CHEMICALS-3.5.175.chemtab.zip>`_
        
        
        
        
        
        
        Dependencies
        ------------
        
        * `ndex2 <https://pypi.org/project/ndex2>`_
        * `ndexutil <https://pypi.org/project/ndexutil>`_
        
        Compatibility
        -------------
        
        * Python 3.3+
        
        Installation
        ------------
        
        .. code-block::
        
           git clone https://github.com/ndexcontent/ndexbiogridloader
           cd ndexbiogridloader
           make dist
           pip install dist/ndexloadbiogrid*whl
        
        
        Run **make** command with no arguments to see other build/deploy options including creation of Docker image
        
        .. code-block::
        
           make
        
        Output:
        
        .. code-block::
        
           clean                remove all build, test, coverage and Python artifacts
           clean-build          remove build artifacts
           clean-pyc            remove Python file artifacts
           clean-test           remove test and coverage artifacts
           lint                 check style with flake8
           test                 run tests quickly with the default Python
           test-all             run tests on every Python version with tox
           coverage             check code coverage quickly with the default Python
           docs                 generate Sphinx HTML documentation, including API docs
           servedocs            compile the docs watching for changes
           testrelease          package and upload a TEST release
           release              package and upload a release
           dist                 builds source and wheel package
           install              install the package to the active Python's site-packages
           dockerbuild          build docker image and store in local repository
           dockerpush           push image to dockerhub
        
        
        Configuration
        -------------
        
        The **ndexloadbiogrid.py** requires a configuration file in the following format be created.
        The default path for this configuration is :code:`~/.ndexutils.conf` but can be overridden with
        :code:`--conf` flag.
        
        **Format of configuration file:**
        
        .. code-block::
        
            [<value in --profile (default ndexbiogridloader)>]
        
            user = <NDEx username>
            password = <NDEx password>
            server = <NDEx server(omit http) ie public.ndexbio.org>
        
        **Example of default configuration file:**
        
        .. code-block::
        
            [ndexbiogridloader]
            user = joe123
            password = somepassword123
            server = dev.ndexbio.org
        
        
        Needed files
        ------------
        
        **TODO:** Add description of needed files
        
        
        Usage
        -----
        
        For information invoke :code:`ndexloadbiogrid.py -h`
        
        The command shown below will download the default version of BioGRID files (3.5.175) to the working
        directory :code:`biogrid_data`, will generate CX networks in this directory, and then upload these networks
        to default account specified in :code:`[ndexbiogridloader]` section of default configuration file:
        
        .. code-block::
        
           ndexloadbiogrid.py biogrid_data
        
        
        Via Docker
        ~~~~~~~~~~~~~~~~~~~~~~
        
        **Example usage**
        
        **TODO:** Add information about example usage
        
        
        .. code-block::
        
           docker run -v `pwd`:`pwd` -w `pwd` vrynkov/ndexbiogridloader:0.1.0 ndexloadbiogrid.py --conf conf # TODO Add other needed arguments here
        
        
        Credits
        -------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        
        =======
        History
        =======
        
        0.1.2 (2019-10-25)
        ------------------
        In organism_load_plan.json, changed types of edge columns
        "Experimental System Type" and "Throughput" to be "list_of_string",
        and "Score" to be "list_of_double".
        This change resolves UD-761 Biogrid network can't be imported to Cytoscape.
        
        0.1.1 (2019-08-23)
        ------------------
        * First release on PyPI.
        
Keywords: ndexbiogridloader
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
