Metadata-Version: 1.1
Name: ndexbiogridloader
Version: 1.0.0
Summary: Loads BioGRID data into NDEx
Home-page: https://github.com/ndexcontent/ndexbiogridloader
Author: Vladimir Rynkov
Author-email: vrynkov@yahoo.edu
License: BSD license
Description: ===========================
        NDEx BioGRID Content Loader
        ===========================
        
        
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                :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-4.2.191.tab2.zip <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.187/BIOGRID-ORGANISM-3.5.87.tab2.zip>`_
        
            `BIOGRID-CHEMICALS-4.2.191.chemtab.zip <https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.187/BIOGRID-CHEMICALS-3.5.187.chemtab.zip>`_
        
        **NOTE:** ``ndexloadbiogrid.py`` script ``--biogridversion`` parameter dictates version (``4.2.191`` above)
        
        
        
        
        
        Dependencies
        ------------
        
        * `ndex2 <https://pypi.org/project/ndex2>`_
        * `ndexutil <https://pypi.org/project/ndexutil>`_
        * `requests <https://pypi.org/project/requests>`_
        * `pandas <https://pypi.org/project/pandas>`_
        * `networkx <https://pypi.org/project/networkx>`_
        * `scipy <https://pypi.org/project/scipy>`_
        * `tqdm <https://pypi.org/project/tqdm>`_
        * `py4cytoscape <https://pypi.org/project/py4cytoscape>`_
        
        Compatibility
        -------------
        
        * Python 3.6+
        
        Installation
        ------------
        
        From PyPi:
        
        .. code-block::
        
           pip install ndexbiogridloader
        
        Build from source:
        
        .. 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
        
        
        
        Usage
        -----
        
        For information invoke :code:`ndexloadbiogrid.py -h`
        
        The command shown below will download the default version of BioGRID files (4.2.191) 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
        
        
        .. note::
        
           By default Cytoscape must be running to generate the layout for each network. See ``--layout`` flag
           options to generate networks without Cytoscape.
        
        
        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
        =======
        
        1.0.0 (11-09-2020)
        ------------------
        
        * New default behavior: **force-directed-cl** layout is now applied on
          networks via py4cytoscape library and a running instance of Cytoscape.
          Alternate Cytoscape layouts and the networkx "spring" layout can be
          run by setting appropriate value via the new **--layout** flag
        
        0.3.0 (10-27-2020)
        ------------------
        
        * Updated default ``--biogridversion`` version to ``4.2.191``
        
        * All generated networks get networkx spring layout added by default
        
        * Added tqdm progress bar support. Set ``--noprogressbar`` flag to disable
        
        * Added --skipupload flag to skip the upload to NDEx step
        
        * Added logic to retry failed upload of network to NDEx.
          ``--maxretries`` and ``--retry_sleep`` allow caller to control
          behavior
        
        * Added ``--organismfile`` and ``--chemicalsfile`` to let caller override
          defaults
        
        0.2.0 (2020-07-27)
        ------------------
        
        * Updated default ``--biogridversion`` version to ``3.5.187``
        
        * Modified organism_list file to include 3 strains of
          coronavirus (SARS-1, SARS-2 and MERS)
        
        * Modified organism_style file to add an orange border
          to all viral protein nodes. This change affects all the
          both new and already existing viral organisms.
        
        0.1.3 (2019-11-21)
        ------------------
        Fixed a bug where networkType used to be a string, now it is a list of strings and we specify 'list_of_string'
        type when setting networkType attribute with network.set_network_attribute("networkType", networkType, 'list_of_string').
        This results in correct representation of networkType in CX model, for example:
        {"n":"networkType","v":["interactome","ppi"],"d":"list_of_string"}.
        
        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 :: 3.6
Classifier: Programming Language :: Python :: 3.7
