Metadata-Version: 2.4
Name: pyrion
Version: 0.2.0
Summary: A fast and efficient bioinformatics library for genomic data processing
Author: Bogdan M. Kirilenko
Maintainer: Bogdan M. Kirilenko
License-Expression: MIT
Project-URL: Homepage, https://github.com/kirilenkobm/pyrion
Project-URL: Repository, https://github.com/kirilenkobm/pyrion
Project-URL: Bug Reports, https://github.com/kirilenkobm/pyrion/issues
Project-URL: Documentation, https://github.com/kirilenkobm/pyrion
Project-URL: Changelog, https://github.com/kirilenkobm/pyrion/releases
Keywords: bioinformatics,genomics,sequence-analysis,comparative-genomics,numpy,alignment,gene-annotation,liftover
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Operating System :: OS Independent
Classifier: Typing :: Typed
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.21.0
Requires-Dist: py2bit>=0.3.0
Requires-Dist: numba>=0.56.0
Provides-Extra: test
Requires-Dist: pytest>=7.0; extra == "test"
Requires-Dist: pytest-cov>=4.0; extra == "test"
Requires-Dist: pytest-xdist>=3.0; extra == "test"
Provides-Extra: visualization
Requires-Dist: matplotlib>=3.5.0; extra == "visualization"
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: pytest-cov>=4.0; extra == "dev"
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Dynamic: license-file

# Pyrion

![PyPI version](https://img.shields.io/badge/version-0.2.0-blue)
![Python](https://img.shields.io/badge/python-3.9%2B-blue)
![License](https://img.shields.io/badge/license-MIT-green)
![Made with Cursor](https://img.shields.io/badge/Made%20with-Cursor-0066cc?style=flat&logo=cursor&logoColor=white)

Tools and abstractions for comparative genomics. Reliable, fast, and minimal-dependency tools 
for common genomics tasks without unnecessary overhead.

Pyrion includes tools for manipulating genomic intervals, genome alignments, and sequences.
It handles common formats like BED (6 or 12), chain, 2bit, and FASTA, and can also parse genePred and GTF annotations.

Work in progress: [plans](TODO.md).

## Installation

```bash
pip install pyrion
```

## Quick Start

See [demo.ipynb](demo.ipynb) for quick examples.

For a more advanced practical example, pls see [TOGA_mini](https://github.com/kirilenkobm/TOGA_mini) repo.

## API Reference

See [API_REFERENCE.md](API_REFERENCE.md) for the complete API documentation.

## License

MIT License - see [LICENSE](LICENSE) file for details.
