snphwe: An exact test of Hardy-Weinberg Equilibrium
Reimplementation in Python of an exact SNP test of Hardy-Weinberg Equilibrium, as described in Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of Hardy-Weinberg Equilibrium. AJHG 76: 887-893.
This package is just a python wrapper around their c implementation.
The simplest way to install snphwe is through pip:
pip install snphwe
Use snphwe within a python environment
from snphwe import snphwe hom1 = 10 hets = 500 hom2 = 5000 hwe_p = snphwe(hets, hom1, hom2)