gadgit 0.7.0
Genetic Algorithm for Disease Gene Identification Toolbox
License: MIT license
Requires Python: >=3.5
Keywords: gadgit

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


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        :target: https://pypi.python.org/pypi/gadgit

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

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        :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.csv', ['Betweenness'], fixed_list=fixed_genes)

        pop, stats, hof = gadgit.ga_multi(gene_info, ga_info)
        ga_output = gadgit.GAoutput(gene_info, ga_info, 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
=======

0.7.0 (2024-08-19)
------------------

* Update dependencies
* Add features to output reports


0.6.0 (2022-08-15)
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* Add multiprocessing support


0.5.0 (2021-08-19)
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* Update to stricter elitism
* Optimize breeding pipeline
* Add better within generation logging
* Fix SoR implementation bug


0.4.0 (2021-05-27)
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* Change frontier to be calculated only based on elite
* Add elite gene ranker to post run script


0.3.0 (2021-05-20)
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* Restructured module
* SoR support
* Error checking
* README updates
* Linting fixes

0.2.1 (2021-03-02)
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* Reformatting of documentation and help page text to pass checks


0.2.0 (2021-03-02)
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* Added documentation on readthedocs
* Abstracted self corrections
* Single point crossover added
* Crossover selection
* Random seed control
* Update requirements


0.1.3 (2021-02-17)
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* 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)
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* Include more packages to build step


0.1.1 (2021-02-17)
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* Fixes to package building


0.1.0 (2021-02-17)
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* First release on PyPI.