Metadata-Version: 2.4
Name: pyrion
Version: 0.3.1
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
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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"
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Dynamic: license-file

# Pyrion

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Pyrion is a lightweight toolkit for comparative genomics focused on fast,
reliable manipulation of genome annotations and alignments.

It provides efficient abstractions for genomic intervals, genome alignment
chains, and sequence access, supporting formats such as BED, chain, 2bit,
FASTA, genePred, and GTF.

Development plans and open tasks are tracked in the [issue tracker](https://github.com/kirilenkobm/pyrion/issues).

## 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.
