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.

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):

pip install bioquik

For developers (editable mode + dev dependencies):

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.

For Users

• Quickstart Guide - Get started quickly
• Validation Guide - Input validation details
• Reports Guide - Understanding output formats

For Developers

• Architecture Guide - System architecture and design decisions
• Module Reference - Detailed module documentation
• Developer Guide - Contributing and extending Bioquik
• Architecture Details - In-depth technical documentation

License

This project is licensed under the terms of the MIT License.

Author