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agct: Another Genome Conversion Tool

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Lift over positions between genomic reference assemblies, 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, Assembly, Strand

c = Converter(Assembly.HG19, Assembly.HG38)

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, 140453137, Strand.POSITIVE)
# returns [LiftoverResult(chrom='chr7', start=140753336, end=140753337, strand=<Strand.POSITIVE: '+'>, score=14633688187)]

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