Another Genome Conversion Tool: Python frontend to Rust chainfile crate
Project description
agct: Another Genome Conversion Tool
Drop-in replacement for the pyliftover tool, using the St. Jude's chainfile crate. Enables significantly faster chainfile loading from cold start (see analysis/).
Status: alpha.
Usage
Initialize a class instance:
from agct import Converter
c = Converter("hg38", "hg19")
Call convert_coordinate():
c.convert_coordinate("chr7", 140453136, "+")
# [['chr7', '140152936', '+']]
Development
The Rust toolchain must be installed.
Create a virtual environment and install developer dependencies:
python3 -m virtualenv venv
source venv/bin/activate
python3 -m pip install -e '.[dev,tests]'
Be sure to install pre-commit hooks:
pre-commit install
This installs Python code as editable, but after any changes to Rust code, maturin develop must be run:
maturin develop
Run tests with pytest:
pytest
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