py1kgp 0.1.2

Utilities for working with 1000 Genomes data

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')