Hierarchical Pangenome toolkit

A toolkit for data convertion and manipulation based on the Hierarchical Pangenome (HAP) model.

Features

• Build a Hierarchical Pangenome from GFA(s)

Requirements

Linux system, bash, gawk installed

Python(>=3.10) and Pip, PostgreSQL

Installation

Install via pip from PyPI:

$ pip install hap

Usage

Database configuration

Initial database configuration through setting environment variables: (Change <username> and <password> to your username and password of the PostgresSQL database to store HAP data)

echo 'export HAP_DB_USER=<username>' >> ~/.bashrc
echo 'export HAP_DB_PASSWORD=<password>' >> ~/.bashrc

or through config:

hap config set db.user <username>
hap config set db.password <password>

See the full list of database configuration in Command-line Reference.

Build a Hierarchical Pangenome

Build from a GFA file:

hap build hprc.gfa -n hprc -a human

or from subgraphs:

hap build hprc_subgraphs/ -n hprc -a human

See the Command-line Reference for details.

Issues

If you encounter any problems, please file an issue along with a detailed description.

Authors

• @yuanminhui

License

This project is under MIT license.

Todos

• Refactor the code into 3-layer DDD-like structure
  • Build classes for HAP and RST model
• Expose CLI & API for dividing GFA into subgraphs to end users
• Add loggings at command level with loguru
• Add tests for commands, classes and module functions
• Add docs (in code, README.md, guide & reference at read the docs)
• Scrutiny and modify dev tooling configs
• Fix poetry installation in Github CI procedure