Metadata-Version: 2.4
Name: bioquik
Version: 0.1.0
Summary: bioquik is a fast and extensible command-line toolkit for counting CG-anchored DNA motifs in FASTA files. Designed to accelerate bioinformatics pipelines with a simple and parallel interface.
Project-URL: Source, https://github.com/Rajkanwars15/bioquik
Project-URL: Documentation, https://github.com/Rajkanwars15/bioquik#readme
Project-URL: Issue Tracker, https://github.com/Rajkanwars15/bioquik/issues
Author-email: Rajkanwar Singh <rajkanwars15@outlook.com>
License: MIT License
        
        Copyright (c) 2025 Rajkanwar Singh
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
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        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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        SOFTWARE.
License-File: LICENSE
Keywords: bioinformatics,fast,fm-index,kmer
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
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Description-Content-Type: text/markdown

# bioquik

**bioquik** is a fast and extensible command-line toolkit for counting CG-anchored DNA motifs in FASTA files. Designed to accelerate bioinformatics pipelines with a simple and parallel interface.

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![Docs](https://img.shields.io/badge/docs-latest-grren?logo=readthedocs)](https://bioquik.readthedocs.io/en/latest/intro.html)
[![GitHub license](https://img.shields.io/github/license/rajkanwars15/bioquik)](https://github.com/Rajkanwars15/bioquik/blob/main/LICENSE)
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[![codecov](https://codecov.io/gh/rajkanwars15/bioquik/branch/main/graph/badge.svg)](https://codecov.io/gh/rajkanwars15/bioquik)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)

[![PyPI - Version](https://img.shields.io/pypi/v/bioquik?logo=pypi)](https://pypi.org/project/bioquik/)
[![Python Versions](https://img.shields.io/badge/python-3.9%20|3.10%20|%203.11|%203.12-blue?logo=python)](https://www.python.org/)
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[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg?logo=contributorcovenant)](code_of_conduct.md)


## Features

- Expand wildcard patterns (e.g. `**CG**`) into exact motifs
- Count motifs using a memory-efficient FM-index
- Parallel processing of multiple FASTA files
- Generates:
  - Per-file CSVs
  - Combined summary CSV
  - Optional JSON summary
  - Optional plots (motif distribution, frequency heatmap)
- Rich progress indicators
- Fully tested with Pytest

## Installation

For **users** (latest release from PyPI):

```bash
pip install bioquik
```

For **developers** (editable mode + dev dependencies):

```bash
git clone https://github.com/Rajkanwars15/bioquik
cd bioquik
pip install -e '.[dev,docs]'
````

## Requirements

* Python ≥ 3.9
* Linux/macOS (tested); Windows should work with minor path adjustments

## Documentation

Full docs are hosted on [Read the Docs](https://bioquik.readthedocs.io/en/latest/).

## License

This project is licensed under the terms of the [MIT License](LICENSE).


## Author

[![Static Badge](https://img.shields.io/badge/Rajkanwars15-yellow?logo=GitHub&link=https%3A%2F%2Fgithub.com%2FRajkanwars15)
](https://www.github.com/rajkanwars15)
