gadgit 0.7.0

Genetic Algorithm for Disease Gene Identification Toolbox

GADGIT

Genetic Algorithm for Disease Gene Identification Toolbox

• Free software: MIT license

• Documentation: https://gadgit.readthedocs.io.

Installation

Via pip:

pip install gadgit

For more information, see the specific installation instructions in the documentation.

Basic Usage

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 GAInfo and GeneInfo classes located on the module docs.

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.

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.