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docs: fill out README #21

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32 changes: 30 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
@@ -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.
<!-- description -->
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/`).
<!-- /description -->

## Installation

Install from [PyPI](https://pypi.org/project/agct/):

```shell
python3 -m pip install agct
```

## Usage

Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down
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