pyphylon

Python package for analyzing and visualizing co-occuring gene / allele sets (phylons) within a pangenome.

Features

• Automated workflows for downloading genomic data from sources like NCBI and BV-BRC.
• Extensive data preprocessing including QC/QA, annotation with tools like bakta, Mash, MLST, and serotype analysis.
• Generation of pangenomes and comprehensive eggNOG annotations.
• Detailed analysis using various forms of normalized and binary data matrices.
• Object-oriented design for extensible and scalable development.

Installation

Clone the repository to your local machine:

git clone https://github.com/yourusername/pyphylon.git

Navigate into the project directory:

cd pyphylon

Install dependencies:

pip install -r requirements.txt

Install pyphylon

pip install -e .

Usage

We recommend working through the example

Running Docker:

1. Build the container with: docker build -t pyphylon .
2. Run the container interactively with: docker run --privileged -it -v %cd%/examples/data:/data -v %cd%/workflow:/workflow pyphylon
3. from INSIDE the container cd to /workflow (cd workflow)
4. Run snakemake with: snakemake -d /data --use-singularity -c 5

Contributing

Contributions are welcome! For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

License

This project is licensed under the MIT License.