Metadata-Version: 2.0
Name: cortexpy
Version: 0.1.1
Summary: The python sister project to CortexJDK
Home-page: https://github.com/winni2k/cortexpy
Author: Warren W. Kretzschmar and Kiran Garimella
Author-email: winni@warrenwk.com and kiran.garimella@gmail.com
License: Apache-2.0
Download-URL: https://github.com/winni2k/cortexpy/archive/0.1.1.tar.gz
Description-Content-Type: UNKNOWN
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.5
Requires-Dist: attrs
Requires-Dist: biopython
Requires-Dist: decorator
Requires-Dist: docopt
Requires-Dist: networkx
Requires-Dist: numpy
Requires-Dist: schema

Cortexpy
========

.. image:: https://travis-ci.org/winni2k/cortexpy.svg?branch=master
  :target: https://travis-ci.org/winni2k/cortexpy
.. image:: https://coveralls.io/repos/github/winni2k/cortexpy/badge.svg?branch=admin_category
  :target: https://coveralls.io/github/winni2k/cortexpy?branch=admin_category
.. image:: https://landscape.io/github/winni2k/cortexpy/master/landscape.svg?style=flat
  :target: https://landscape.io/github/winni2k/cortexpy/master

Supporting Python versions 3.5 and 3.6.

Cortexpy is a Python package for sequence analysis using linked and colored de Bruijn graphs such as
the ones created by `Mccortex <https://github.com/mcveanlab/mccortex>`_.
This project aims to mirror many of the features contained in
`CortexJDK <https://github.com/mcveanlab/CortexJDK>`_.


Install
-------

Install the latest version of cortexpy::

    pip install cortexpy

Bugs
----

Please raise a github issue for any bugs.

Development
-----------

Set up the project::

    make init

See `cortexpy/__main__.py` for example uses of cortexpy.

Publishing to Pypi
------------------

::

    # assuming version 0.0.1

    # Step 1: Set __version__ in cortexpy/__init__.py

    # Step 2: Make version commit
    git commit -am'Bump to version 0.0.1'

    # Step 3: tag commit
    git tag 0.0.1

    # Step 4: publish to pypi
    make deploy



