annotate average_fst.py @ 24:248b06e86022

Added gd_genotype datatype. Modified tools to support new datatype.

#!/usr/bin/env python

import sys
import subprocess
from Population import Population

################################################################################

if len(sys.argv) < 12:
    print >> sys.stderr, "Usage"
    sys.exit(1)

input, p1_input, p2_input, input_type, data_source, min_total_count, discard_fixed, output, shuffles, p0_input = sys.argv[1:11]
individual_metadata = sys.argv[11:]

try:
    shuffle_count = int(shuffles)
except:
    shuffle_count = 0

p_total = Population()
p_total.from_tag_list(individual_metadata)

p1 = Population()
p1.from_population_file(p1_input)
if not p_total.is_superset(p1):
    print >> sys.stderr, 'There is an individual in population 1 that is not in the SNP table'
    sys.exit(1)

p2 = Population()
p2.from_population_file(p2_input)
if not p_total.is_superset(p2):
    print >> sys.stderr, 'There is an individual in population 2 that is not in the SNP table'
    sys.exit(1)

p0 = None
if shuffle_count > 0:
    p0 = Population()
    p0.from_population_file(p0_input)
    if not p_total.is_superset(p0):
        print >> sys.stderr, 'There is an individual in population 0 that is not in the SNP table'
        sys.exit(1)

################################################################################

prog = 'Fst_ave'

args = []
args.append(prog)
args.append(input)
args.append(data_source)
args.append(min_total_count)
args.append(discard_fixed)
args.append(shuffles)

columns = p1.column_list()
for column in columns:
    if input_type == 'gd_genotype':
        column = int(column) - 2
    args.append('{0}:1'.format(column))

columns = p2.column_list()
for column in columns:
    if input_type == 'gd_genotype':
        column = int(column) - 2
    args.append('{0}:2'.format(column))

if p0 is not None:
    columns = p0.column_list()
    for column in columns:
        if input_type == 'gd_genotype':
            column = int(column) - 2
        args.append('{0}:0'.format(column))

fh = open(output, 'w')

#print "args:", ' '.join(args)
p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
rc = p.wait()
fh.close()

sys.exit(0)