Metadata-Version: 2.4
Name: diempy
Version: 1.0.2
Summary: Polarize genomes using diem
Author: Stuart J.E. Baird
Author-email: Derek Setter <derek.setter@gmail.com>
License-Expression: GPL-3.0
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy<=2.3,>=1.20.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: numba>=0.56.0
Requires-Dist: matplotlib>=3.4.0
Requires-Dist: docopt>=0.6.2
Requires-Dist: scikit-allel>=1.3.0
Requires-Dist: joblib>=1.5.3
Requires-Dist: ipympl>=0.10.0
Requires-Dist: pysam>=0.23.3
Dynamic: license-file

## diemPy

A Python package for genome polarization and subsequent analyses using the `diem` (Diagnostic Index for the Expectation Maximization) method [1]

## Overview

`diemPy` is a computational tool designed to polarize genomic data for hybrid zone analysis. The package implements an expectation-maximization (EM) algorithm to determine the optimal polarization of genetic markers, enabling researchers to identify and analyze patterns of introgression and hybridization in genomic datasets.



## Key Features
- VCF processing and format conversion
- Automated genome polarization using EM algorithm
- Kernel smoothing and tract length analysis
- Parallel processing support
- Flexible I/O for various genomic formats


## Documentation

The core concepts, installation, and API documentation can be found here:

📚 **[Introduction, Installation, and API Documentation](https://diempy.readthedocs.io/en/latest/intro.html)**

The primary documentation for using `diemPy` is provided as a self-guided tutorial with an example dataset:

📚 **[Tutorial](https://github.com/DerekSetter/tutorial-DiemPy)**


## License

This project is licensed under the GPL-3.0 License - see the [LICENSE](LICENSE) file for details.

## Author

Derek Setter, Stuart J.E. Baird

## Citation
[1] Baird, S. J. E., Petružela, J., Jaroň, I., Škrabánek, P., & Martínková, N. (2023). Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution, 14, 512–528. https://doi.org/10.1111/2041-210X.14010
