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/).

Installation

Install from PyPI:

python3 -m pip install agct

Usage

Initialize a class instance:

from agct import Converter, Genome
c = Converter(Genome.HG38, Genome.HG19)

If a chainfile is unavailable locally, it's downloaded from UCSC and saved using the wags-tails package -- see the wags-tails configuration instructions for information on how to designate a non-default storage location.

Call convert_coordinate():

c.convert_coordinate("chr7", 140453136, "+")
# [['chr7', 140152936, <Strand.POSITIVE: '+'>]]

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]'

This installs Python code as editable, but after any changes to Rust code, run maturin develop to rebuild the Rust binary:

maturin develop

Be sure to install pre-commit hooks:

pre-commit install

Check Python style with ruff:

python3 -m ruff format . && python3 -m ruff check --fix .

Use cargo fmt to check Rust style (must be run from within the rust/ subdirectory):

cd rust/
cargo fmt

Run tests with pytest:

pytest