genesets (Python)
Python bindings for genesets-rs. The compute runs in Rust and releases the GIL.
import genesets
result = genesets.mgsa(
annotations=[("BRCA1", "GO:0006281"), ...], # (gene, term), propagated to ancestors
study=["BRCA1", "RAD51", ...],
background=None, # default: every annotated gene
closure=[("GO:0006281", "GO:0006974"), ...], # optional (child, ancestor) pairs
)
for term in result["terms"][:10]:
print(term["id"], term["posterior"], term["overlap"], term["term_size"])
mgsa is Bayesian model-based gene set analysis, as in Ontologizer and
wtfgenes. Each term gets a posterior probability of being active, so ancestors
of an enriched term are explained away instead of being reported alongside it.
Keyword options match the genesets-rs mgsa CLI (samples_per_term,
burn_per_term, the *_prob/*_count priors, move rates, and seed).
Install
Until wheels are on PyPI, install from git. Building from source needs a Rust toolchain:
uv add "genesets @ git+https://github.com/monarch-initiative/genesets#subdirectory=python/genesets-py"
Develop
cd python/genesets-py
uv run --with maturin --with pytest maturin develop --release
uv run --with pytest pytest tests
Release
Publish a GitHub release whose tag is the version, such as v0.2.0 (or
v0.2.0-rc.1 for a pre-release, which PyPI lists as 0.2.0rc1). The
Python wheels workflow builds wheels for Linux, macOS and Windows plus an
sdist, sets the package version from the tag, and uploads to PyPI through
trusted publishing in the pypi environment. No version bump is committed
first; the version in Cargo.toml here only matters for local builds.
1 maintainer
Metadata
1 maintainer
Release files for genesets 0.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| genesets-0.1.1.tar.gz | 56.8 kB | With provenance | Details for genesets-0.1.1.tar.gz |
Built distributions (wheels)
| File | Actions Reset | |||
|---|---|---|---|---|
| genesets-0.1.1-cp310-abi3-win_amd64.whl | CPython 3.10 | abi3 | Windows x86-64 | Details for genesets-0.1.1-cp310-abi3-win_amd64.whl |
| genesets-0.1.1-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ x86-64 | Details for genesets-0.1.1-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
| genesets-0.1.1-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ ARM64 | Details for genesets-0.1.1-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
| genesets-0.1.1-cp310-abi3-macosx_11_0_arm64.whl | CPython 3.10 | abi3 | macOS 11.0+ ARM64 | Details for genesets-0.1.1-cp310-abi3-macosx_11_0_arm64.whl |
| genesets-0.1.1-cp310-abi3-macosx_10_12_x86_64.whl | CPython 3.10 | abi3 | macOS 10.12+ x86-64 | Details for genesets-0.1.1-cp310-abi3-macosx_10_12_x86_64.whl |
Total release size: 1.7 MB
Release files / genesets-0.1.1.tar.gz
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