cbgen
Python wrapper around a BGEN library. (cbgen documentation).
BGEN is a file format for storing large genetic datasets. It supports both unphased genotypes and phased haplotype data with variable ploidy and number of alleles. It was designed to provide a compact data representation without sacrificing variant access performance. This Python package is a wrapper around the bgen library, a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats.
Installation
pip install cbgen
Usage example
>>> import cbgen
>>>
>>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen"))
>>> bgen.create_metafile("haplotypes.bgen.metafile")
>>> mf = cbgen.bgen_metafile("haplotypes.bgen.metafile")
>>> print(mf.npartitions)
1
>>> print(mf.nvariants)
4
>>> print(mf.partition_size)
4
>>> part = mf.read_partition(0)
>>> gt = bgen.read_genotype(part.variants.offset[0])
>>> print(gt.probability)
[[1. 0. 1. 0.]
[0. 1. 1. 0.]
[1. 0. 0. 1.]
[0. 1. 0. 1.]]
>>> mf.close()
>>> bgen.close()
Authors
License
This project is licensed under the MIT License.
1 maintainer
Metadata
1 maintainer
Release files for cbgen 1.0.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| cbgen-1.0.6.tar.gz | 12.4 kB | Details |
Built distributions (wheels)
Total release size: 9.3 MB
Release files / cbgen-1.0.6.tar.gz
| Download URL | cbgen-1.0.6.tar.gz |
|---|---|
| Size | 12.4 kB |
| Tags | Source |
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Release files / cbgen-1.0.6-cp312-cp312-win_amd64.whl
| Download URL | cbgen-1.0.6-cp312-cp312-win_amd64.whl |
|---|---|
| Size | 319.7 kB |
| Tags | CPython 3.12 Windows x86-64 |
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Release files / cbgen-1.0.6-cp312-cp312-musllinux_1_2_x86_64.whl
| Download URL | cbgen-1.0.6-cp312-cp312-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 914.9 kB |
| Tags | CPython 3.12 Linux musl 1.2+ x86-64 |
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| Download URL | cbgen-1.0.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 767.5 kB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 |
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Release files / cbgen-1.0.6-cp312-cp312-macosx_14_0_arm64.whl
| Download URL | cbgen-1.0.6-cp312-cp312-macosx_14_0_arm64.whl |
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| Size | 380.3 kB |
| Tags | CPython 3.12 macOS 14.0+ ARM64 |
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| Download URL | cbgen-1.0.6-cp311-cp311-win_amd64.whl |
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| Download URL | cbgen-1.0.6-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Download URL | cbgen-1.0.6-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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| Download URL | cbgen-1.0.6-cp310-cp310-win_amd64.whl |
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| Download URL | cbgen-1.0.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Download URL | cbgen-1.0.6-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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Release files / cbgen-1.0.6-cp39-cp39-macosx_13_0_x86_64.whl
| Download URL | cbgen-1.0.6-cp39-cp39-macosx_13_0_x86_64.whl |
|---|---|
| Size | 149.9 kB |
| Tags | CPython 3.9 macOS 13.0+ x86-64 |
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SHA-256 checksum How to use checksums |
f32275bbd77c32a40129e0d37450de019f74fefecdd337217116d1a4cdf21713
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BLAKE2b-256 checksum How to use checksums |
9ad4207566dd60778e5c868dc887bddc0cc20a9c4ebdb06bd451669d12064ef7
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.0 CPython/3.12.4
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