genoio
genoio reads VCF/BCF, PLINK1, PLINK2, and BGEN genotype sources into Python
matrices. The public API is Python; the file readers are Rust. This pairing
keeps the interface simple while moving parsing and matrix construction into
compiled, efficient code.
It is built for downstream genetics tools that need stable matrix contracts: samples on rows, variants on columns, and metadata aligned to returned matrices, blocks, or regions.
Install
To install the most recent release:
pip install genoio
Or the latest:
pip install git+https://github.com/mancusolab/genoio.git
Documentation
For complete documentation and examples, see the documentation site.
Quick Example
import genoio
ds = genoio.pfile("data/chr22_hg38")
samples = ds.samples()
y = load_phenotype_vector(samples["iid"])
C = load_covariates(samples["iid"])
with ds.iter_blocks(10_000, return_variants=True) as blocks:
for X, variants in blocks:
# X has shape (samples, variants_in_this_block).
# `y` and `C` must be aligned to the rows described by `samples`.
association_scan(X, y, C, variants=variants)
Use read(...) for one matrix, iter_blocks(...) for streaming scans, and
iter_regions(...) for interval-based workflows.
License
MIT. See LICENSE.
Notes
genoio was developed by members of the Mancuso Lab with assistance from Codex,
following the practices described in the
scientific-software-playbook
and coding-skills repositories.
1 maintainer
Metadata
1 maintainer
Release files for genoio 0.4.1
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 | |
|---|---|---|---|---|
| genoio-0.4.1.tar.gz | 264.6 kB | With provenance | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| genoio-0.4.1-cp314-cp314-manylinux_2_28_x86_64.whl | CPython 3.14 | CPython 3.14 | Linux glibc 2.28+ x86-64 | Details |
| genoio-0.4.1-cp314-cp314-macosx_11_0_arm64.whl | CPython 3.14 | CPython 3.14 | macOS 11.0+ ARM64 | Details |
| genoio-0.4.1-cp313-cp313-manylinux_2_28_x86_64.whl | CPython 3.13 | CPython 3.13 | Linux glibc 2.28+ x86-64 | Details |
| genoio-0.4.1-cp313-cp313-macosx_11_0_arm64.whl | CPython 3.13 | CPython 3.13 | macOS 11.0+ ARM64 | Details |
| genoio-0.4.1-cp312-cp312-manylinux_2_28_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.28+ x86-64 | Details |
| genoio-0.4.1-cp312-cp312-macosx_11_0_arm64.whl | CPython 3.12 | CPython 3.12 | macOS 11.0+ ARM64 | Details |
| genoio-0.4.1-cp311-cp311-manylinux_2_28_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.28+ x86-64 | Details |
| genoio-0.4.1-cp311-cp311-macosx_11_0_arm64.whl | CPython 3.11 | CPython 3.11 | macOS 11.0+ ARM64 | Details |
Total release size: 38.3 MB
Release files / genoio-0.4.1.tar.gz
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