pybcf

This is a package for reading BCF files (binary call format). Similar to pysam/cyvcf2, but limited to reading from BCF files only, and oriented around getting genotype data into numpy arrays quickly.

This performs relatively better at larger sample sizes e.g. it's 7X faster than pysam with 2k samples, but improves to 50X faster than pysam with 30k samples. Currently it's slower than pysam for BCFs without sample level data, but BCFs without genotypes aren't generally a limiting factor e.g. it still parses 300k variants/second under those conditions.

from pybcf import BcfReader

bcf = BcfReader(bcf_path)

sample_ids = bcf.samples
contigs = bcf.header.contigs

for var in bcf:
    # the usual attributes are available e.g.
    # var.chrom, var.pos, var.ref, var.alts, var.info['AF']
    
    # sample data is accessed as numpy arrays via the format keys
    keys = list(var.samples)
    genotypes = var.samples['GT']  # as n x 2 numpy array, missing=nan

# or fetch from random regions if bcf is indexed
for var in bcf.fetch('chr1', 10000, 200000):
    print(var.chrom, var.pos)

Limitations

  • doesn't work with uncompressed BCFs
  • extracting info fields is a little slow

Project links

Key dates

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  • Released:
Latest release

1 maintainer

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Avatar for jeremy.mcrae from gravatar.com jeremy.mcrae

Credits

Author: Jeremy McRae

License

MIT

Provides Extra

test

Classifiers

Report project as malware

Metadata

Project links

Key dates

PyPI data
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  • Released:
Latest release

1 maintainer

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Avatar for jeremy.mcrae from gravatar.com jeremy.mcrae

Credits

Author: Jeremy McRae

License

MIT

Provides Extra

test

Classifiers

Report project as malware

Release files for pybcf 1.3.7

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pybcf-1.3.7-cp314-cp314-win_amd64.whl 200.7 kB CPython 3.14 CPython 3.14 Windows x86-64 Details
pybcf-1.3.7-cp314-cp314-musllinux_1_2_x86_64.whl 3.1 MB CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details
pybcf-1.3.7-cp314-cp314-musllinux_1_2_aarch64.whl 3.0 MB CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details
pybcf-1.3.7-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 2.1 MB CPython 3.14 CPython 3.14 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
pybcf-1.3.7-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 2.1 MB CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-64 Details
pybcf-1.3.7-cp314-cp314-macosx_11_0_arm64.whl 211.1 kB CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
pybcf-1.3.7-cp313-cp313-win_amd64.whl 194.4 kB CPython 3.13 CPython 3.13 Windows x86-64 Details
pybcf-1.3.7-cp313-cp313-musllinux_1_2_x86_64.whl 3.1 MB CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details
pybcf-1.3.7-cp313-cp313-musllinux_1_2_aarch64.whl 3.0 MB CPython 3.13 CPython 3.13 Linux musl 1.2+ ARM64 Details
pybcf-1.3.7-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 2.1 MB CPython 3.13 CPython 3.13 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
pybcf-1.3.7-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 2.1 MB CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-64 Details
pybcf-1.3.7-cp313-cp313-macosx_11_0_arm64.whl 210.6 kB CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
pybcf-1.3.7-cp312-cp312-win_amd64.whl 194.6 kB CPython 3.12 CPython 3.12 Windows x86-64 Details
pybcf-1.3.7-cp312-cp312-musllinux_1_2_x86_64.whl 3.2 MB CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details
pybcf-1.3.7-cp312-cp312-musllinux_1_2_aarch64.whl 3.0 MB CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details
pybcf-1.3.7-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 2.1 MB CPython 3.12 CPython 3.12 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
pybcf-1.3.7-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 2.1 MB CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details
pybcf-1.3.7-cp312-cp312-macosx_11_0_arm64.whl 211.1 kB CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
pybcf-1.3.7-cp311-cp311-win_amd64.whl 193.6 kB CPython 3.11 CPython 3.11 Windows x86-64 Details
pybcf-1.3.7-cp311-cp311-musllinux_1_2_x86_64.whl 3.1 MB CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details
pybcf-1.3.7-cp311-cp311-musllinux_1_2_aarch64.whl 3.0 MB CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details
pybcf-1.3.7-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 2.1 MB CPython 3.11 CPython 3.11 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
pybcf-1.3.7-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 2.0 MB CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details
pybcf-1.3.7-cp311-cp311-macosx_11_0_arm64.whl 210.5 kB CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
pybcf-1.3.7-cp310-cp310-win_amd64.whl 193.3 kB CPython 3.10 CPython 3.10 Windows x86-64 Details
pybcf-1.3.7-cp310-cp310-musllinux_1_2_x86_64.whl 3.1 MB CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-64 Details
pybcf-1.3.7-cp310-cp310-musllinux_1_2_aarch64.whl 3.0 MB CPython 3.10 CPython 3.10 Linux musl 1.2+ ARM64 Details
pybcf-1.3.7-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 2.0 MB CPython 3.10 CPython 3.10 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
pybcf-1.3.7-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 2.0 MB CPython 3.10 CPython 3.10 Linux glibc 2.17+ x86-64 Details
pybcf-1.3.7-cp310-cp310-macosx_11_0_arm64.whl 210.6 kB CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
pybcf-1.3.7-cp39-cp39-win_amd64.whl 193.8 kB CPython 3.9 CPython 3.9 Windows x86-64 Details
pybcf-1.3.7-cp39-cp39-musllinux_1_2_x86_64.whl 3.1 MB CPython 3.9 CPython 3.9 Linux musl 1.2+ x86-64 Details
pybcf-1.3.7-cp39-cp39-musllinux_1_2_aarch64.whl 3.0 MB CPython 3.9 CPython 3.9 Linux musl 1.2+ ARM64 Details
pybcf-1.3.7-cp39-cp39-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 2.0 MB CPython 3.9 CPython 3.9 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
pybcf-1.3.7-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 2.0 MB CPython 3.9 CPython 3.9 Linux glibc 2.17+ x86-64 Details
pybcf-1.3.7-cp39-cp39-macosx_11_0_arm64.whl 211.0 kB CPython 3.9 CPython 3.9 macOS 11.0+ ARM64 Details
pybcf-1.3.7-cp38-cp38-win_amd64.whl 194.6 kB CPython 3.8 CPython 3.8 Windows x86-64 Details
pybcf-1.3.7-cp38-cp38-musllinux_1_2_x86_64.whl 3.1 MB CPython 3.8 CPython 3.8 Linux musl 1.2+ x86-64 Details
pybcf-1.3.7-cp38-cp38-musllinux_1_2_aarch64.whl 3.0 MB CPython 3.8 CPython 3.8 Linux musl 1.2+ ARM64 Details
pybcf-1.3.7-cp38-cp38-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 2.1 MB CPython 3.8 CPython 3.8 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
pybcf-1.3.7-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 2.0 MB CPython 3.8 CPython 3.8 Linux glibc 2.17+ x86-64 Details
pybcf-1.3.7-cp38-cp38-macosx_11_0_arm64.whl 158.7 kB CPython 3.8 CPython 3.8 macOS 11.0+ ARM64 Details

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