Skip to main content

Bgen file format reader

Project description

bgen-reader

Travis AppVeyor Gitter

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bgen_reader-1.1.1.tar.gz (1.3 MB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page