# 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.

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## 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)
