======
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.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)
------------------
* Add multiprocessing support
0.5.0 (2021-08-19)
------------------
* Update to stricter elitism
* Optimize breeding pipeline
* Add better within generation logging
* Fix SoR implementation bug
0.4.0 (2021-05-27)
------------------
* Change frontier to be calculated only based on elite
* Add elite gene ranker to post run script
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.
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"description": "======\nGADGIT\n======\n\n\n.. image:: https://img.shields.io/pypi/v/gadgit.svg\n :target: https://pypi.python.org/pypi/gadgit\n\n.. image:: https://img.shields.io/travis/Andesha/gadgit.svg\n :target: https://travis-ci.com/Andesha/gadgit\n\n.. image:: https://readthedocs.org/projects/gadgit/badge/?version=latest\n :target: https://gadgit.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n\n\n\nGenetic Algorithm for Disease Gene Identification Toolbox\n\n\n* Free software: MIT license\n* Documentation: https://gadgit.readthedocs.io.\n\n\nInstallation\n----------------\n\nVia `pip`:\n\n:code:`pip install gadgit`\n\nFor more information, see the specific installation instructions in the `documentation <https://gadgit.readthedocs.io/en/latest/installation.html>`_.\n\nBasic Usage\n----------------\n\n.. code-block:: python\n\n import gadgit\n\n ga_info = gadgit.GAInfo()\n\n fixed_genes = ['BRCA1', 'AR', 'ATM', 'CHEK2', 'BRCA2', 'STK11', 'RAD51', 'PTEN', 'BARD1', 'TP53', 'RB1CC1', 'NCOA3', 'PIK3CA', 'PPM1D', 'CASP8']\n gene_info = gadgit.GeneInfo('brca.csv', ['Betweenness'], fixed_list=fixed_genes)\n\n pop, stats, hof = gadgit.ga_multi(gene_info, ga_info)\n ga_output = gadgit.GAoutput(gene_info, ga_info, hof)\n\nCustomization 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>`_.\n\nFeatures\n----------------\n\n* Multi objective support\n* Evolutionary algorithm parameter selection\n* Dynamic bioinformatics settings\n* Variable community size\n* Generational statistics\n* Post processing helpers\n* Centrality builders\n* HPC ready\n\nCredits\n----------------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n\n=======\nHistory\n=======\n\n0.7.0 (2024-08-19)\n------------------\n\n* Update dependencies\n* Add features to output reports\n\n\n0.6.0 (2022-08-15)\n------------------\n\n* Add multiprocessing support\n\n\n0.5.0 (2021-08-19)\n------------------\n\n* Update to stricter elitism\n* Optimize breeding pipeline\n* Add better within generation logging\n* Fix SoR implementation bug\n\n\n0.4.0 (2021-05-27)\n------------------\n\n* Change frontier to be calculated only based on elite\n* Add elite gene ranker to post run script\n\n\n0.3.0 (2021-05-20)\n------------------\n\n* Restructured module\n* SoR support\n* Error checking\n* README updates\n* Linting fixes\n\n0.2.1 (2021-03-02)\n------------------\n\n* Reformatting of documentation and help page text to pass checks\n\n\n0.2.0 (2021-03-02)\n------------------\n\n* Added documentation on readthedocs\n* Abstracted self corrections\n* Single point crossover added\n* Crossover selection\n* Random seed control\n* Update requirements\n\n\n0.1.3 (2021-02-17)\n------------------\n\n* Fix more build bugs\n* Expose post processing function\n* Clean up string representation of parameter classes\n* Add fixed genes support\n* Add more assertions for debugging\n* Made mutation respect fixed genes structure\n* Updated test dataframe\n\n\n0.1.2 (2021-02-17)\n------------------\n\n* Include more packages to build step\n\n\n0.1.1 (2021-02-17)\n------------------\n\n* Fixes to package building\n\n\n0.1.0 (2021-02-17)\n------------------\n\n* First release on PyPI.\n\n\n",
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