Metadata-Version: 2.5
Name: liulab-genome
Version: 2026.8.0
Summary: Handling reference genome related tasks.
Project-URL: Homepage, https://github.com/lhqing/liulab-genome
Project-URL: Issues, https://github.com/lhqing/liulab-genome/issues
Project-URL: Changelog, https://github.com/lhqing/liulab-genome/blob/main/CHANGELOG.md
Author: Liu Lab
License-Expression: MIT
License-File: LICENSE
Keywords: bedtools,bioinformatics,genomics,samtools
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Python: >=3.12
Requires-Dist: numpy>=2
Requires-Dist: pandas<3,>=2.1
Requires-Dist: pooch>=1.8
Requires-Dist: py2bit>=0.3
Requires-Dist: requests>=2.31
Requires-Dist: tqdm>=4
Requires-Dist: typer>=0.12
Description-Content-Type: text/markdown

# liulab-genome

Reference genomes on disk, ready to query. Name an assembly and it is fetched, prepared
(`.fai`, `.2bit`, `chrom.sizes`) and answering sequence queries — plus GTF annotations
registered against it and STAR/chromap indexes built from it.

Import name: `genome`.

```python
from genome import Genome

sacCer3 = Genome("sacCer3")
sacCer3.fetch_sequence("chrIV:0-10")   # DNA('ACACCACACC') — 0-based, half-open
```

Docs: <https://liuhlab.github.io/liulab-genome/>

## Development

This project uses [pixi](https://pixi.sh) with `conda-forge` + `bioconda` channels. Native
deps (`samtools`, `bedtools`) and Python tooling are all managed by pixi.

```bash
pixi install                     # solve & install the default env (resolves from pixi.lock if present)
pixi shell                       # activate the env
pixi run check                   # lint + fmt-check + typecheck + test, run concurrently (the gate)
pixi run -e aligners test-aligner # the other lane: the tests that build a real STAR/chromap index
```

See [`AGENTS.md`](./AGENTS.md) (`CLAUDE.md` symlinks to it) for the full contributor/agent working agreement.

## License

MIT — see [`LICENSE`](./LICENSE).
