Metadata-Version: 1.1
Name: PyBEL
Version: 0.3.1
Summary: Parsing, validation, and analysis of BEL graphs
Home-page: https://github.com/pybel/pybel
Author: Charles Tapley Hoyt
Author-email: charles.hoyt@scai.fraunhofer.de
License: Apache 2.0 License
Description: PyBEL
        =====
        
        :code:`PyBEL` is a Python software package that parses BEL scripts, validates their semantics, applies common graph
        algorithms, and facilitates data interchange between common formats and database systems like JSON, CSV, SQL, and Neo4J.
        
        Development:
        
        =========== =============== ================== =======================
        Stable      |stable_build|  |stable_coverage|  |stable_documentation| 
        Development |develop_build| |develop_coverage| |develop_documentation|
        =========== =============== ================== =======================
        
        
        .. |stable_build| image:: https://travis-ci.org/pybel/pybel.svg?branch=master
            :target: https://travis-ci.org/pybel/pybel
            :alt: Stable Build Status
        
        .. |stable_coverage| image:: https://codecov.io/gh/pybel/pybel/coverage.svg?branch=master
            :target: https://codecov.io/gh/pybel/pybel?branch=master
            :alt: Stable Coverage Status
        
        .. |stable_documentation| image:: https://readthedocs.org/projects/pybel/badge/?version=stable
            :target: http://pybel.readthedocs.io/en/stable/
            :alt: Stable Documentation Status
        
        .. |develop_build| image:: https://travis-ci.org/pybel/pybel.svg?branch=develop
            :target: https://travis-ci.org/pybel/pybel
            :alt: Development Build Status
        
        .. |develop_coverage| image:: https://codecov.io/gh/pybel/pybel/coverage.svg?branch=develop
            :target: https://codecov.io/gh/pybel/pybel?branch=develop
            :alt: Development Coverage Status
        
        .. |develop_documentation| image:: https://readthedocs.org/projects/pybel/badge/?version=latest
            :target: http://pybel.readthedocs.io/en/latest/
            :alt: Development Documentation Status
        
        .. |climate| image:: https://codeclimate.com/github/pybel/pybel/badges/gpa.svg
            :target: https://codeclimate.com/github/pybel/pybel
            :alt: Code Climate
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/PyBEL.svg
            :alt: Stable Supported Python Versions
        	
        .. |pypi_version| image:: https://img.shields.io/pypi/v/PyBEL.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/PyBEL.svg
            :alt: Apache 2.0 License
        
        
        Biological Expression Language (BEL) is a domain specific language that enables the expression of complex molecular
        relationships and their context in a machine-readable form. Its simple grammar and expressive power have led to its
        successful use in the `IMI <https://www.imi.europa.eu/>`_ project, `AETIONOMY <http://www.aetionomy.eu/>`_, to describe
        complex disease networks with several thousands of relationships.
        
        :code:`PyBEL` provides a simple API so bioinformaticians and scientists with limited programming knowledge can easily
        use it to interface with BEL graphs, but is built on a rich framework that can be extended to develop new algorithms.
        
        .. code-block:: python
        
           >>> import pybel, networkx
           >>> g = pybel.from_url('http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel')
           >>> networkx.draw(g)  # NOTE: requires matplotlib as a dependency, which isn't automatically installed
        
        Command Line Interface
        ----------------------
        
        PyBEL also installs a command line interface with the command :code:`pybel` for simple utilities such as data
        conversion. Need help? All logs go to :code:`~/.pybel` or add :code:`-v` for verbose output to the standard error
        stream
        
        Export for Cytoscape
        ~~~~~~~~~~~~~~~~~~~~
        
        This example retrieves a BEL file from a path and exports to a GraphML file for use in Cytoscape.
        
        .. code-block:: sh
        
            $ pybel convert --path ~/Desktop/example.bel --graphml ~/Desktop/example.graphml
           
        In Cytoscape, open with :code:`Import > Network > From File`.
        
        Export to Neo4j
        ~~~~~~~~~~~~~~~
        
        This example retrieves a BEL file from a URL, and exports to Neo4j
        
        .. code-block:: sh
        
           $ URL="http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel"
           $ NEO="neo4j:neo4j@localhost:7474"
           $
           $ pybel convert --url $URL --neo $NEO
        
        Multiple Export
        ~~~~~~~~~~~~~~~
        
        This example gets a file from stdin and exports to multiple locations, with logging
        
        .. code-block:: sh
        
           $ URL="http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel"
           $ NEO="neo4j:neo4j@localhost:7474"
           $
           $ curl $URL | pybel convert --neo $NEO --json ~/Desktop/example.json --log-file ~/Desktop/log.txt
        
        Installation
        ------------
        
        |pypi_version| |python_versions| |pypi_license|
        
        
        PyBEL can be installed easily from `PyPI <https://pypi.python.org/pypi/pybel>`_ with the following code in
        your favorite terminal:
        
        .. code-block:: sh
        
           pip install pybel
        
        See the `documentation <http://pybel.readthedocs.io/>`_ for more advanced instructions.
        
        Contributing
        ------------
        
        Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
        :code:`CONTRIBUTING.rst` for more information on getting involved.
        
        Acknowledgements
        ----------------
        
        - This software is proudly built with Paul McGuire's `PyParsing <http://pyparsing.wikispaces.com/>`_ package.
        - `Scott Colby <https://github.com/scolby33>`_ designed our `logo <https://github.com/pybel/pybel-art>`_ and provided sage advice
        - Core Team: `Charles Tapley Hoyt <https://github.com/cthoyt>`_, `Andrej Konotopez <https://github.com/lekono>`_, and `Christian Ebeling <https://github.com/cebel>`_
        
        Links
        -----
        
        - Specified by `BEL 1.0 <http://openbel.org/language/web/version_1.0/bel_specification_version_1.0.html>`_ and
          `BEL 2.0 <http://openbel.org/language/web/version_2.0/bel_specification_version_2.0.html>`_
        - Documented on `Read the Docs <http://pybel.readthedocs.io/>`_
        - Versioned on `GitHub <https://github.com/pybel/pybel>`_
        - Tested on `Travis CI <https://travis-ci.org/pybel/pybel>`_
        - Distributed by `PyPI <https://pypi.python.org/pypi/pybel>`_
        - Chat on `Gitter <https://gitter.im/pybel/Lobby>`_
        
Keywords: Biological Expression Language,BEL,Systems Biology,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
