bwtools

A Python package for working with bigWig files and analyzing genomic data.

Installation

Install from PyPI:

pip install bwtools

Or install from source:

git clone https://github.com/gspracklin/bwtools.git
cd bwtools
pip install -e .

Requirements

• Python 3.4+
• Dependencies:
  • bioframe
  • click
  • matplotlib
  • numpy
  • pandas
  • pomegranate
  • pybbi
  • cytoolz

Usage

bwtools provides several commands for analyzing bigWig files:

Call Domains

Use Hidden Markov Models (HMM) to call domains from bigWig signal:

bwtools call_domains -g hg38 -n 2 --output domains input.bw

Options:

• --genome/-g: Genome assembly (e.g. hg38)
• --num-states/-n: Number of HMM states (default: 2)
• --cmap: Colormap for visualization (default: coolwarm)
• --sparse: Merge neighboring bins with same state
• --output/-o: Output filename

Compute Regions

Calculate mean signal values in specified regions:

bwtools compute_regions --bigwigs file1.bw,file2.bw --bedfiles regions1.bed,regions2.bed --plot output.png

Options:

• --bigwigs: Comma-separated list of bigWig files
• --bedfiles: Comma-separated list of BED files defining regions
• --plot: Optional output plot filename

License

This project is licensed under the MIT License - see the LICENSE file for details.

Author

George Spracklin

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.