while parent is not None and parent.time < time:
if parent.parent is not None and parent.parent.time < time:
parent = parent.parent
else:
break
if parent is None:
return hit
else:
return parent
def build_tree(f, args, chrom, pop_sizes):
for line in f:
# Skip over a line, which contains the seed for a simulation run.
line = f.next()
data = eval(line)
for r in range(args.reps):
generate_trees(data[chrom],
args.size1,
args.size2,
pop_sizes,
args.internal)
if __name__ == '__main__':
parser = parse_common_arguments('Construct gene tree.')
parser.add_argument('-i', '--internal',
action = 'store_true',
help = 'output names of internal nodes')
run(parser.parse_args(), build_tree)
if coal_gen.count(i) == 2][0]
unchanged = [0, 0]
for s1 in coal_gen[:size1]:
if s1 < pop_size / 2 and s1 != merged:
unchanged[0] += 1
for s2 in coal_gen[size1:]:
if s2 < pop_size / 2 and s2 != merged:
unchanged[1] += 1
merged1 = coal_gen.index(merged)
merged2 = coal_gen.index(merged, merged1 + 1)
if merged1 < size1 and merged2 < size1:
ctype = 0
elif merged1 < size1:
ctype = 1
else:
ctype = 2
if merged < pop_size / 2:
deme = 1
else:
deme = 2
print('{}, {}, {}, {}, {}'.format(
time, unchanged[0], unchanged[1], deme, ctype))
return True
if __name__ == '__main__':
run(parse_common_arguments('Summarize coalescence time and exit states').parse_args(), get_exit_states)
