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)
def main():
"""
Main CLI handler.
"""
parser = argparse.ArgumentParser()
parser.add_argument("-f",
"--format",
dest="schema",
type=str,
default="nexus",
choices=["nexus", "newick"],
help="input data format (default='%(default)s')")
parser.add_argument("-l",
"--label",
type=str,
default="[TESTING]",
help="label for test")
parser.add_argument(
"-r",
"--regime",
dest="regime",
type=str,
default="mean",
choices=[
"mean-coalescent", "converse-coalescent", "uniform-coalescent"
],
help=
"expected regime under which the coalescent intervals were generated (default='%(default)s')"
)
parser.add_argument("-p",
"--precision",
type=float,
default=0.01,
help="numerical precision (default=%(default)s)")
args = parser.parse_args()
fails = 0
trees = dendropy.TreeList.get_from_stream(sys.stdin, schema=args.schema)
for tidx, tree in enumerate(trees):
tree_fails = 0
# check structure
if not tree._debug_tree_is_valid():
sys.stderr.write("{} Tree {}: structure is invalid".format(
args.label, tidx + 1))
tree_fails += 1
# ensure parent ages > child ages
tree.calc_node_ages(check_prec=args.precision)
for nd in tree.postorder_node_iter():
if nd.parent_node is not None:
if nd.age > nd.parent_node.age:
sys.stderr.write(
"{} Tree {}: Node '{}': age ({}) is greater than parent age ({})"
.format(args.label, tidx + 1, nd.label, nd.age,
nd.parent_node.age))
tree_fails += 1
# check waiting times
num_tips = len(tree.leaf_nodes())
wf = coalescent.extract_coalescent_frames(
tree, check_ultrametricity_prec=args.precision)
num_lineages = sorted(wf.keys())
for n in num_lineages:
wt = wf[n]
if args.regime == "mean-coalescent":
exp_wt = coalescent.expected_tmrca(n)
elif args.regime == "converse-coalescent":
exp_wt = coalescent.expected_tmrca(num_tips - n + 2)
elif args.regime == "uniform-coalescent":
exp_wt = 1.0
else:
raise RuntimeError("Unsupported regime: '{}'".format(
args.regime))
if abs(exp_wt - wt) > args.precision:
sys.stderr.write(
"{} Tree {}: Waiting time for coalescence event with {} lineages: expecting {} but found {}\n"
.format(args.label, tidx + 1, n, exp_wt, wt))
tree_fails += 1
if tree_fails > 0:
sys.stderr.write("{} Tree {} failed: {}\n".format(
args.label, tidx + 1, tree.compose_newick()))
fails += tree_fails
if fails > 0:
sys.exit(1)
else:
sys.exit(0)
def main():
"""
Main CLI handler.
"""
parser = argparse.ArgumentParser()
parser.add_argument("-f", "--format",
dest="schema",
type=str,
default="nexus",
choices=["nexus", "newick"],
help="input data format (default='%(default)s')")
parser.add_argument("-l", "--label",
type=str,
default="[TESTING]",
help="label for test")
parser.add_argument("-r", "--regime",
dest="regime",
type=str,
default="mean",
choices=["mean-coalescent", "converse-coalescent", "uniform-coalescent"],
help="expected regime under which the coalescent intervals were generated (default='%(default)s')")
parser.add_argument("-p", "--precision",
type=float,
default=0.01,
help="numerical precision (default=%(default)s)")
args = parser.parse_args()
fails = 0
trees = dendropy.TreeList.get_from_stream(sys.stdin, schema=args.schema)
for tidx, tree in enumerate(trees):
tree_fails = 0
# check structure
if not tree._debug_tree_is_valid():
sys.stderr.write("{} Tree {}: structure is invalid".format(args.label, tidx+1))
tree_fails += 1
# ensure parent ages > child ages
tree.calc_node_ages(check_prec=args.precision)
for nd in tree.postorder_node_iter():
if nd.parent_node is not None:
if nd.age > nd.parent_node.age:
sys.stderr.write("{} Tree {}: Node '{}': age ({}) is greater than parent age ({})".format(
args.label, tidx+1, nd.label, nd.age, nd.parent_node.age))
tree_fails += 1
# check waiting times
num_tips = len(tree.leaf_nodes())
wf = coalescent.extract_coalescent_frames(tree, check_ultrametricity_prec=args.precision)
num_lineages = sorted(wf.keys())
for n in num_lineages:
wt = wf[n]
if args.regime == "mean-coalescent":
exp_wt = coalescent.expected_tmrca(n)
elif args.regime == "converse-coalescent":
exp_wt = coalescent.expected_tmrca(num_tips - n + 2)
elif args.regime == "uniform-coalescent":
exp_wt = 1.0
else:
raise RuntimeError("Unsupported regime: '{}'".format(args.regime))
if abs(exp_wt - wt) > args.precision:
sys.stderr.write("{} Tree {}: Waiting time for coalescence event with {} lineages: expecting {} but found {}\n".format(
args.label, tidx+1, n, exp_wt, wt))
tree_fails += 1
if tree_fails > 0:
sys.stderr.write("{} Tree {} failed: {}\n".format(args.label, tidx+1, tree.compose_newick()))
fails += tree_fails
if fails > 0:
sys.exit(1)
else:
sys.exit(0)
