def num_segregating_sites(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.num_segregating_sites(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.num_segregating_sites(...)",
)
return popgenstat.num_segregating_sites(char_matrix, ignore_uncertain)
def num_segregating_sites(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.num_segregating_sites(...)",
new_construct=
"from dendropy.calculate import popgenstat\npopgenstat.num_segregating_sites(...)",
)
return popgenstat.num_segregating_sites(char_matrix, ignore_uncertain)
def test_num_segregating_sites(self):
self.assertEqual(popgenstat.num_segregating_sites(self.data, ignore_uncertain=True), 183)
def test_num_segregating_sites(self):
self.assertEqual(
popgenstat.num_segregating_sites(self.data, ignore_uncertain=True),
183)
# -*- 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")
#!/usr/bin/env python3
import dendropy
import dendropy.calculate.popgenstat as pgs
import sys
if len(sys.argv) < 2:
print("usage: %s alignment.fasta" % sys.argv[0], file=sys.stderr)
sys.exit(0)
# read alignment
alignment_fasta = sys.argv[1]
char_mat = dendropy.DnaCharacterMatrix.get(file=open(alignment_fasta), schema='fasta')
# calculate stats
n_seg_sites = pgs.num_segregating_sites(char_mat)
# report
print("segregating sites:\t%d" % n_seg_sites)
