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.

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 with conda-forge + bioconda channels. Native deps (samtools, bedtools) and Python tooling are all managed by pixi.

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 (CLAUDE.md symlinks to it) for the full contributor/agent working agreement.

License

MIT — see LICENSE.

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Credits

Author: Liu Lab

License expression

MIT
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Requires

Python >=3.12

Tags

bedtools bioinformatics genomics samtools

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