popgenstats-example.py

#! /usr/bin/env python


import dendropy
from dendropy.calculate import popgenstat

d = dendropy.DnaCharacterMatrix.get_from_path(
        "data/primates.chars.nexus", "nexus")
print("num_segregating_sites = {}".format(popgenstat.num_segregating_sites(d, True)))
print("num_segregating_sites = {}".format(popgenstat.num_segregating_sites(d, False)))
print("average_number_of_pairwise_differences = {}".format(popgenstat.average_number_of_pairwise_differences(d, True)))
print("average_number_of_pairwise_differences = {}".format(popgenstat.average_number_of_pairwise_differences(d, False)))
print("nucleotide_diversity = {}".format(popgenstat.nucleotide_diversity(d, True)))
print("nucleotide_diversity = {}".format(popgenstat.nucleotide_diversity(d, False)))
print("tajimas_d = {}".format(popgenstat.tajimas_d(d, True)))
print("tajimas_d = {}".format(popgenstat.tajimas_d(d, False)))
print("wattersons_theta = {}".format(popgenstat.wattersons_theta(d, True)))
print("wattersons_theta = {}".format(popgenstat.wattersons_theta(d, False)))
print("derived_state_matrix = {}".format(popgenstat.derived_state_matrix(d)))
print("unfolded_site_frequency_spectrum = {}".format(popgenstat.unfolded_site_frequency_spectrum(d)))