def wattersons_theta(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.watterson_theta(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.watterson_theta(...)",
)
return popgenstat.wattersons_theta(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
def wattersons_theta(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.watterson_theta(...)",
new_construct=
"from dendropy.calculate import popgenstat\npopgenstat.watterson_theta(...)",
)
return popgenstat.wattersons_theta(char_matrix=char_matrix,
ignore_uncertain=ignore_uncertain)
def test_wattersons_theta(self):
self.assertAlmostEqual(popgenstat.wattersons_theta(self.data, ignore_uncertain=True), 49.00528, 4)
def test_wattersons_theta(self):
self.assertAlmostEqual(
popgenstat.wattersons_theta(self.data, ignore_uncertain=True),
49.00528, 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")