Bgen file format reader
Project description
bgen-reader
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A BGEN file format <http://www.well.ox.ac.uk/~gav/bgen_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 <https://github.com/limix/bgen>
__, 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 <https://conda.io/docs/>
__
.. code:: bash
conda install -c conda-forge bgen
Alternatively, the bgen-reader repository <https://github.com/limix/bgen>
__ provides instructions for
manual installation.
Once bgen C library is installed, simply enter
.. code:: bash
pip install bgen-reader
from the command-line.
Usage
It is as simple as
.. code:: python
# 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 <https://github.com/limix/bgen-reader-py/issues/new>
__.
Authors
Danilo Horta <https://github.com/horta>
__
License
This project is licensed under the MIT License <https://raw.githubusercontent.com/limix/bgen-reader-py/master/LICENSE.md>
__.
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