diff --git a/README.md b/README.md index d513810..3c7ab2b 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,21 @@ # agct: Another Genome Conversion Tool -Drop-in replacement for the [pyliftover](https://github.com/konstantint/pyliftover) tool, using the St. Jude's [chainfile](https://docs.rs/chainfile/latest/chainfile/) crate. Enables significantly faster chainfile loading from cold start (see `analysis/`). +[![image](https://img.shields.io/pypi/v/agct.svg)](https://pypi.python.org/pypi/agct) +[![image](https://img.shields.io/pypi/l/agct.svg)](https://pypi.python.org/pypi/agct) +[![image](https://img.shields.io/pypi/pyversions/agct.svg)](https://pypi.python.org/pypi/agct) +[![Actions status](https://github.com/genomicmedlab/agct/workflows/CI/badge.svg)](https://github.com/genomicmedlab/agct/actions) -Status: alpha. + +A drop-in replacement for the [pyliftover](https://github.com/konstantint/pyliftover) tool, using the St. Jude's [chainfile](https://docs.rs/chainfile/latest/chainfile/) crate. Enables significantly faster chainfile loading from cold start (see `analysis/`). + + +## Installation + +Install from [PyPI](https://pypi.org/project/agct/): + +```shell +python3 -m pip install agct +``` ## Usage @@ -13,6 +26,8 @@ from agct import Converter c = Converter("hg38", "hg19") ``` +> If a chainfile is unavailable locally, it's downloaded from UCSC and saved using the `wags-tails` package -- see the [configuration instructions](https://github.com/GenomicMedLab/wags-tails?tab=readme-ov-file#configuration) for information on how to designate a non-default storage location. + Call ``convert_coordinate()``: ```python3 @@ -44,6 +59,19 @@ This installs Python code as editable, but after any changes to Rust code, ``mat maturin develop ``` +Check Python style with `ruff`: + +```shell +python3 -m ruff format . && python3 -m ruff check --fix . +``` + +Use `cargo fmt` to check Rust style (must be run from within the `rust/` subdirectory): + +```shell +cd rust/ +cargo fmt +``` + Run tests with `pytest`: ```shell