Metadata-Version: 1.2
Name: cortexpy
Version: 0.46.4
Summary: The python sister project to CortexJDK
Home-page: https://github.com/winni2k/cortexpy
Author: Warren W. Kretzschmar, Kiran V Garimella
Author-email: winni@warrenwk.com, kiran.garimella@gmail.com
License: Apache-2.0
Download-URL: https://github.com/winni2k/cortexpy/archive/0.46.4.tar.gz
Description: Overview of Cortexpy_
        =====================
        
        .. start-badges
        
        .. list-table::
            :stub-columns: 1
        
            * - tests
              - | |travis|
                | |coveralls| |codecov|
            * - package
              - | |version| |wheel| |supported-versions|
                | |supported-implementations| |commits-since|
            * - docs
              - | |readthedocs|
        
        .. |travis| image:: https://travis-ci.org/winni2k/cortexpy.svg?branch=master
            :alt: Travis-CI Build Status
            :target: https://travis-ci.org/winni2k/cortexpy
        
        .. |coveralls| image:: https://coveralls.io/repos/winni2k/cortexpy/badge.svg?branch=master&service=github
            :alt: Coverage Status
            :target: https://coveralls.io/r/winni2k/cortexpy
        
        .. |codecov| image:: https://codecov.io/github/winni2k/cortexpy/coverage.svg?branch=master
            :alt: Coverage Status
            :target: https://codecov.io/github/winni2k/cortexpy
        
        .. |version| image:: https://img.shields.io/pypi/v/cortexpy.svg
            :alt: PyPI Package latest release
            :target: https://pypi.python.org/pypi/cortexpy
        
        .. |commits-since| image:: https://img.shields.io/github/commits-since/winni2k/cortexpy/v0.46.4.svg
            :alt: Commits since latest release
            :target: https://github.com/winni2k/cortexpy/compare/v0.46.4...master
        
        .. |wheel| image:: https://img.shields.io/pypi/wheel/cortexpy.svg
            :alt: PyPI Wheel
            :target: https://pypi.python.org/pypi/cortexpy
        
        .. |supported-versions| image:: https://img.shields.io/pypi/pyversions/cortexpy.svg
            :alt: Supported versions
            :target: https://pypi.python.org/pypi/cortexpy
        
        .. |supported-implementations| image:: https://img.shields.io/pypi/implementation/cortexpy.svg
            :alt: Supported implementations
            :target: https://pypi.python.org/pypi/cortexpy
        
        .. |readthedocs| image:: https://readthedocs.org/projects/cortexpy/badge/?version=latest
           :target: https://cortexpy.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        
        
        .. end-badges
        
        Cortexpy is a Python package for sequence analysis using linked and colored De Bruijn graphs such as
        the ones created by Cortex_ and Mccortex_.
        This project aims to mirror many of the features contained in
        `CortexJDK <https://github.com/mcveanlab/CortexJDK>`_.
        
        .. _cortexpy: https://github.com/winni2k/cortexpy
        
        Cortexpy also comes with a command-line tool for basic inspection and manipulation of Cortex graphs with and without links.
        
        .. _Cortex: https://github.com/iqbal-lab/cortex
        .. _Mccortex: https://github.com/mcveanlab/mccortex
        
        Audience
        --------
        
        The audience of cortexpy is researchers working with colored De Bruijn graphs and link information in Cortex_ and Mccortex_ format.
        
        
        Free software
        -------------
        
        Cortexpy is free software; you can redistribute it and/or modify it under the
        terms of the Apache License version 2.0.  Contributions are welcome. Please join us on `GitHub <https://github.com/winni2k/cortexpy>`_.
        
        
        Installation
        ------------
        
        ::
        
            pip install cortexpy
        
        
        Documentation
        -------------
        
        For more information, please see cortexpy documentation_.
        
        .. _documentation: https://cortexpy.readthedocs.io/en/latest/index.html
        
        Citing cortexpy
        ---------------
        
        If you use cortexpy in your work, please consider citing:
        
            Akhter, Shirin, Warren W. Kretzschmar, Veronika Nordal, Nicolas Delhomme, Nathaniel R. Street, Ove Nilsson, Olof Emanuelsson, and Jens F. Sundström. "Integrative analysis of three RNA sequencing methods identifies mutually exclusive exons of MADS-box isoforms during early bud development in *Picea abies*." *Frontiers in Plant Science* 9 (2018). https://doi.org/10.3389/fpls.2018.01625
        
        Bugs
        ----
        
        This code is maintained by Warren Kretzschmar <warrenk@kth.se>.
        For bugs, please raise a `GitHub issue <https://github.com/winni2k/cortexpy/issues>`_.
        
        Development
        -----------
        
        1. Install `conda <https://docs.conda.io/en/latest/miniconda.html>`_.
        2. Download development and testing tools::
        
            conda env create -f environment.yml -n my-dev-environment
        
        3. Activate development environment::
        
            conda activate my-dev-environment
        
        All remaining commands in the development section need to be run in an activated
        conda dev environment.
        
        
        
        Tests
        `````
        
        ::
        
            make test
        
        Deploy new cortexpy version to pypi
        ```````````````````````````````````
        
        Requires access credentials for pypi.
        
        ::
        
            make deploy
        
        Building the docs
        `````````````````
        
        The documentation is automatically built by read-the-docs on push to master.
        To build the documentation manually::
        
            # install sphinx dependencies
            pip install docs/requirements.txt
        
            make docs
        
        Updating the dev environment
        ````````````````````````````
        
        This section is experimental because it does not work on travis-CI yet.
        
        ::
        
            # Create a new env from the high-level requirements file
            conda env create -f environment.yml -n another-dev-env
        
            # activate the new environment
            conda activate another-dev-env
        
            # save new env to environment.lock.yml
            make lock
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: Implementation :: CPython
Requires-Python: >=3.6
