def main():
"""
Main CLI handler.
"""
parser = OptionParser(usage=_prog_usage,
add_help_option=True,
version=_prog_version,
description=_prog_description)
parser.add_option('-n', '--pop-size', '-N',
action='store',
dest='pop_size',
type='int',
default=1,
metavar='Ne',
help='effective HAPLOID population size (default=%default [assumes edge lengths are in units of Ne])')
(opts, args) = parser.parse_args()
if len(args) == 0:
sys.stderr.write("%s" % parser.get_usage())
sys.exit(1)
for a in args:
fpath = os.path.expandvars(os.path.expanduser(a))
if not os.path.exists(fpath):
sys.stderr.write('File not found: "%s"\n' % fpath)
else:
sys.stderr.write('Reading: "%s"\n' % fpath)
d = datasets.Dataset()
ctrees = d.read_trees(open(fpath, "rU"), "NEXUS")
for t in ctrees:
p = coalescent.log_probability_of_coalescent_tree(t, opts.pop_size)
sys.stdout.write("%s\n" % p)
def testSimple1(self):
t = dendropy.Tree.get_from_string("((((a:1, b:1):1, c:2):1, d:3, e:3):2, (f:4, g:4):1)", "newick")
i1 = coalescent.node_waiting_time_pairs(t)
assert [x[1] for x in i1] == [1.0, 1.0, 1.0, 1.0, 1.0]
i2 = coalescent.extract_coalescent_frames(t)
assert i2 == {7: 1.0, 6:1.0, 5:1.0, 3:1.0, 2:1.0}
check = coalescent.log_probability_of_coalescent_tree(t, 10)
def testSimple1(self):
t = dendropy.Tree.get_from_string(
"((((a:1, b:1):1, c:2):1, d:3, e:3):2, (f:4, g:4):1)", "newick")
i1 = coalescent.node_waiting_time_pairs(t)
assert [x[1] for x in i1] == [1.0, 1.0, 1.0, 1.0, 1.0]
i2 = coalescent.extract_coalescent_frames(t)
assert i2 == {7: 1.0, 6: 1.0, 5: 1.0, 3: 1.0, 2: 1.0}
check = coalescent.log_probability_of_coalescent_tree(t, 10)
