def average_number_of_pairwise_differences(char_matrix, ignore_uncertain=True): deprecate.dendropy_deprecation_warning( preamble="The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.", old_construct="from dendropy import popgenstat\npopgenstat.average_number_of_pairwise_differences(...)", new_construct="from dendropy.calculate import popgenstat\npopgenstat.average_number_of_pairwise_differences(...)", ) return popgenstat.average_number_of_pairwise_differences(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
def average_number_of_pairwise_differences(char_matrix, ignore_uncertain=True): deprecate.dendropy_deprecation_warning( preamble= "The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.", old_construct= "from dendropy import popgenstat\npopgenstat.average_number_of_pairwise_differences(...)", new_construct= "from dendropy.calculate import popgenstat\npopgenstat.average_number_of_pairwise_differences(...)", ) return popgenstat.average_number_of_pairwise_differences( char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
def test_average_number_of_pairwise_differences(self): self.assertAlmostEqual(popgenstat.average_number_of_pairwise_differences(self.data, ignore_uncertain=True), 62.75000, 4)
def test_average_number_of_pairwise_differences(self): self.assertAlmostEqual( popgenstat.average_number_of_pairwise_differences( self.data, ignore_uncertain=True), 62.75000, 4)
# -*- coding: utf-8 -*- "run as python estimate_SFS_stats.py $inputfile" "Appends to the given output file" import dendropy from dendropy.calculate import popgenstat import os import sys seqs = dendropy.DnaCharacterMatrix.get(path=sys.argv[1], schema="fasta") out = open("popgen_stats.txt", "a") pop = sys.argv[1].split("/")[1].split("_")[2].split(".")[0] gene = sys.argv[1].split("/")[1].split("_")[0] fbtr = sys.argv[1].split("/")[1].split("_")[1] td = popgenstat.tajimas_d(seqs) tw = popgenstat.wattersons_theta(seqs) tp = popgenstat.average_number_of_pairwise_differences(seqs) ss = popgenstat.num_segregating_sites(seqs) out.write("\t".join( [str(pop), str(gene), str(fbtr), str(td), str(tw), str(tp), str(ss)]) + "\n")