Metadata-Version: 2.1
Name: bio2bel-kegg
Version: 0.0.7.dev0
Summary: A wraper around the KEGG RESTful API
Home-page: https://github.com/bio2bel/kegg
Author: Daniel Domingo-Fernández and Charles Tapley Hoyt
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
Maintainer: Daniel Domingo-Fernández and Charles Tapley Hoyt
Maintainer-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: MIT License
Platform: UNKNOWN
Provides-Extra: web
Requires-Dist: click
Requires-Dist: requests
Requires-Dist: bio2bel (>=0.0.9)
Requires-Dist: compath-utils (>=0.0.2)
Requires-Dist: bio2bel-hgnc (>=0.0.4)
Requires-Dist: pybel (>=0.11.1)
Requires-Dist: sqlalchemy
Requires-Dist: pandas
Requires-Dist: tqdm
Provides-Extra: web
Requires-Dist: flask; extra == 'web'
Requires-Dist: flask-admin; extra == 'web'

Bio2BEL KEGG |build| |coverage| |documentation| |zenodo|
========================================================
This package allows the enrichment of BEL networks with KEGG information by wrapping its RESTful API.
Furthermore, it is integrated in the `ComPath environment <https://github.com/ComPath>`_ for pathway database comparison.

Installation |pypi_version| |python_versions| |pypi_license|
------------------------------------------------------------
``bio2bel_kegg`` can be installed easily from `PyPI <https://pypi.python.org/pypi/bio2bel_kegg>`_ with the
following code in your favorite terminal:

.. code-block:: sh

    $ python3 -m pip install bio2bel_kegg

or from the latest code on `GitHub <https://github.com/bio2bel/kegg>`_ with:

.. code-block:: sh

    $ python3 -m pip install git+https://github.com/bio2bel/kegg.git@master

Setup
-----
KEGG can be downloaded and populated from either the Python REPL or the automatically installed command line utility.

The following resources will be automatically installed and loaded in order to fully populate the tables of the
database:

- `Bio2BEL HGNC <https://github.com/bio2bel/hgnc>`_

Python REPL
~~~~~~~~~~~
.. code-block:: python

    >>> import bio2bel_kegg
    >>> kegg_manager = bio2bel_kegg.Manager()
    >>> kegg_manager.populate()

Command Line Utility
~~~~~~~~~~~~~~~~~~~~
.. code-block:: bash

    bio2bel_kegg populate

Other Command Line Utilities
----------------------------
- Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_kegg web` (http://localhost:5000/admin/)
- Export gene sets for programmatic use :code:`python3 -m bio2bel_kegg export`

Citation
--------
- Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017).
- Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
- Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

.. |build| image:: https://travis-ci.org/bio2bel/kegg.svg?branch=master
    :target: https://travis-ci.org/bio2bel/kegg
    :alt: Build Status

.. |coverage| image:: https://codecov.io/gh/bio2bel/kegg/coverage.svg?branch=master
    :target: https://codecov.io/gh/bio2bel/kegg?branch=master
    :alt: Coverage Status

.. |documentation| image:: http://readthedocs.org/projects/bio2bel-interpro/badge/?version=latest
    :target: http://bio2bel.readthedocs.io/projects/kegg/en/latest/?badge=latest
    :alt: Documentation Status

.. |climate| image:: https://codeclimate.com/github/bio2bel/kegg/badges/gpa.svg
    :target: https://codeclimate.com/github/bio2bel/kegg
    :alt: Code Climate

.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_kegg.svg
    :alt: Stable Supported Python Versions

.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_kegg.svg
    :alt: Current version on PyPI

.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_kegg.svg
    :alt: MIT License

.. |zenodo| image:: https://zenodo.org/badge/105248163.svg
    :target: https://zenodo.org/badge/latestdoi/105248163


