Metadata-Version: 2.1
Name: gadgit
Version: 0.3.0
Summary: Genetic Algorithm for Disease Gene Identification Toolbox
Home-page: https://github.com/Andesha/gadgit
Author: Tyler Collins
Author-email: tk11br@sharcnet.ca
License: MIT license
Keywords: gadgit
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.5
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: deap

======
GADGIT
======


.. image:: https://img.shields.io/pypi/v/gadgit.svg
        :target: https://pypi.python.org/pypi/gadgit

.. image:: https://img.shields.io/travis/Andesha/gadgit.svg
        :target: https://travis-ci.com/Andesha/gadgit

.. image:: https://readthedocs.org/projects/gadgit/badge/?version=latest
        :target: https://gadgit.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status




Genetic Algorithm for Disease Gene Identification Toolbox


* Free software: MIT license
* Documentation: https://gadgit.readthedocs.io.


Installation
----------------

Via `pip`:

:code:`pip install gadgit`

For more information, see the specific installation instructions in the `documentation <https://gadgit.readthedocs.io/en/latest/installation.html>`_.

Basic Usage
----------------

.. code-block:: python

        import gadgit

        ga_info = gadgit.GAInfo()

        fixed_genes = ['BRCA1', 'AR', 'ATM', 'CHEK2', 'BRCA2', 'STK11', 'RAD51', 'PTEN', 'BARD1', 'TP53', 'RB1CC1', 'NCOA3', 'PIK3CA', 'PPM1D', 'CASP8']
        gene_info = gadgit.GeneInfo('brca.pkl', ['Betweenness'], fixed_list=fixed_genes)

        pop, stats, hof = gadgit.ga_single(gene_info, ga_info)
        gadgit.post_run(gene_info, ga_info, pop, stats, hof)

Customization of parameters can be found in the class documentation of the :code:`GAInfo` and :code:`GeneInfo` classes located `on the module docs <https://gadgit.readthedocs.io/en/latest/api/gadgit.html#module-gadgit.GAInfo>`_.

Features
----------------

* Multi objective support
* Evolutionary algorithm parameter selection
* Dynamic bioinformatics settings
* Variable community size
* Generational statistics
* Post processing helpers
* Centrality builders
* HPC ready

Credits
----------------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

0.3.0 (2021-05-20)
------------------

* Restructured module
* SoR support
* Error checking
* README updates
* Linting fixes

0.2.1 (2021-03-02)
------------------

* Reformatting of documentation and help page text to pass checks


0.2.0 (2021-03-02)
------------------

* Added documentation on readthedocs
* Abstracted self corrections
* Single point crossover added
* Crossover selection
* Random seed control
* Update requirements


0.1.3 (2021-02-17)
------------------

* Fix more build bugs
* Expose post processing function
* Clean up string representation of parameter classes
* Add fixed genes support
* Add more assertions for debugging
* Made mutation respect fixed genes structure
* Updated test dataframe


0.1.2 (2021-02-17)
------------------

* Include more packages to build step


0.1.1 (2021-02-17)
------------------

* Fixes to package building


0.1.0 (2021-02-17)
------------------

* First release on PyPI.


