cbgen 1.0.4

Python wrapper around a BGEN library

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

• Carl Kadie
• Danilo Horta

License

This project is licensed under the MIT License.