PLINK file processing with numba
Project description
microplink
This class provides a minimal and fast interface for retrieving genotypes from Plinks's BED/BIM/FAM file trios. The BED file must fit in memory.
Requirements
numpy
, pandas
, and numba
. These are included with many Python
distributions.
Installation
Run pip install microplink
or clone this repository and run python setup.py install
from the repository directory.
Usage
Typical usage:
import microplink as mic
# Equivalent to `pf = mic.PlinkFiles('test.bed', 'test.bim', 'test.fam')`
pf = mic.PlinkFiles('test')
# fetch by chromosome and position
pf.get_genotypes(chromosome=1, position=10000)
# fetch by variant name (often RSID)
pf.get_genotypes(snp='rs1235123')
# fetch by SNP integer index
pf.get_genotypes(snp_index=0)
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