py1kgp

Utilities for working with 1000 Genomes data

Installation

First make sure you have followed the installation procedure for pydbsnp. Then install py1kgp with pip3:

pip3 install py1kgp

or

pip3 install --user py1kgp

For full functionality, you should appropriately set the environment variable PY1KGP_DIR. For example, you could add this to your .bash_profile:

export PY1KGP_DIR=<path to directory of your choice>

Examples

import py1kgp
py1kgp.Variant('rs10')
py1kgp.Variant(id='rs10')
py1kgp.Variant(7, 92383888)
py1kgp.Variant(chrom=7, pos=92383888)
py1kgp.fast_genotypes(7, 92383888)
py1kgp.fast_genotypes(7, 92383888, samples='NA21142,NA21143,NA21144')
py1kgp.fast_maf(7, 92383888)
py1kgp.slice_vcf(1, 1000000, 2000000)
py1kgp.slice_vcf(1, 1000000, 2000000, samples='NA21142,NA21143,NA21144')
py1kgp.slice_vcf(1, 1000000, 2000000, samples='AFR')
py1kgp.slice_vcf(1, 1000000, 2000000, samples='samples.panel')