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)