Bgen file format reader

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Project description

bgen-reader

Travis AppVeyor

A BGEN file format reader.

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 provides 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.

Install

It requires the bgen C library which can be installed via conda

conda install -c conda-forge bgen

Alternatively, the bgen-reader repository provides instructions for manual installation.

Once bgen C library is installed, simply enter

pip install bgen-reader

from the command-line.

Usage

It is as simple as

# example.py file
from bgen_reader import read_bgen

bgen = read_bgen("example.bgen", verbose=False)

print(bgen['variants'].head())
print(bgen['samples'].head())
print(len(bgen['genotype']))
print(bgen['genotype'][0].compute())

The output should something similar to

chrom       id  nalleles   pos    rsid
0    01  SNPID_2         2  2000  RSID_2
1    01  SNPID_3         2  3000  RSID_3
2    01  SNPID_4         2  4000  RSID_4
3    01  SNPID_5         2  5000  RSID_5
4    01  SNPID_6         2  6000  RSID_6
         id
0  sample_001
1  sample_002
2  sample_003
3  sample_004
4  sample_005
199
[[        nan         nan         nan]
[ 0.02780236  0.00863674  0.9635609 ]
[ 0.01736504  0.04968414  0.93295083]
...,
[ 0.01419069  0.02810669  0.95770262]
[ 0.91949463  0.05206298  0.02844239]
[ 0.00244141  0.98410029  0.0134583 ]]

Problems

If you encounter any issue, please, submit it.

Authors

License

This project is licensed under the MIT License.

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