Metadata-Version: 1.1
Name: PyBEL
Version: 0.2.5
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 statements, validates their semantics, applies common graph
        algorithms, and allows for data interchange between common formats like Neo4J, JSON, CSV, Excel, and SQL.
        
        =========== =============== ================== ======================= ====================
        Stable      |stable_build|  |stable_coverage|  |stable_documentation|  |stable_pyversions|
        Development |develop_build| |develop_coverage| |develop_documentation| |develop_pyversions|
        =========== =============== ================== ======================= ====================
        
        
        .. |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
        
        .. |stable_pyversions| image::  https://img.shields.io/pypi/pyversions/PyBEL.svg
            :alt: Stable Supported Python Versions
        
        .. |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
        
        .. |develop_pyversions| image:: https://img.shields.io/badge/python-2.7%2C%203.5-blue.svg
            :alt: Development Supported Python Versions
        
        .. |climate| image:: https://codeclimate.com/github/pybel/pybel/badges/gpa.svg
            :target: https://codeclimate.com/github/pybel/pybel
            :alt: Code Climate
        
        
        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.
        
        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)
        
        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 --path - --neo $NEO --json ~/Desktop/example.json --log-file ~/Desktop/log.txt
        
        Installation
        ------------
        
        Installation is as easy as running from your favorite terminal:
        
        .. code-block:: sh
        
           pip install pybel
        
        Currently, :code:`PyBEL` officially supports Python 2.7 and Python 3.5. Builds also pass on Python 3.4, and there
        are some problems that can be solved with the installation of :code:`pandas` for Python 3.3 usage.
        
        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
        ----------------
        
        - PyBEL is proudly built with Paul McGuire's PyParsing package.
        - Scott Colby designed our logo and provided sage advice
        - PyBEL Core Team: Charles Tapley Hoyt, Andrej Konotopez, Christian Ebeling
        
        Find Us
        -------
        
        - `Read the Docs <http://pybel.readthedocs.io/>`_
        - `GitHub <https://github.com/pybel/pybel>`_
        - `PyPI <https://pypi.python.org/pypi/pybel>`_
        - `Chat on Gitter <https://gitter.im/pybel/Lobby>`_
        
Keywords: Fraunhofer,SCAI,BEL
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 :: 3.5
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
