def get_species_tree(self, ntax=10):
_RNG = MockRandom()
ages = [_RNG.randint(1000,10000) for age in range(ntax)]
ages.sort()
pop_sizes = [_RNG.randint(1000,10000) for pop in range(2*ntax+1)]
taxon_namespace = dendropy.TaxonNamespace(["t{}".format(i+1) for i in range(ntax)])
species_tree = popgensim.pop_gen_tree(taxon_namespace=taxon_namespace,
ages=ages,
num_genes=4,
pop_sizes=pop_sizes,
rng=_RNG)
ages2 = []
for node in species_tree.postorder_node_iter():
distance_from_tip = node.distance_from_tip()
if distance_from_tip > 0:
ages2.append(distance_from_tip)
ages2.sort()
for index in range(len(ages2)):
assert (ages[index] - ages2[index]) < 10e-6
pop_sizes2 = []
for edge in species_tree.postorder_edge_iter():
pop_sizes2.append(edge.pop_size)
pop_sizes2.sort()
return species_tree
def get_species_tree(self, ntax=10):
_RNG = MockRandom()
ages = [_RNG.randint(1000, 10000) for age in range(ntax)]
ages.sort()
pop_sizes = [_RNG.randint(1000, 10000) for pop in range(2 * ntax + 1)]
taxon_namespace = dendropy.TaxonNamespace(
["t{}".format(i + 1) for i in range(ntax)])
species_tree = popgensim.pop_gen_tree(taxon_namespace=taxon_namespace,
ages=ages,
num_genes=4,
pop_sizes=pop_sizes,
rng=_RNG)
ages2 = []
for node in species_tree.postorder_node_iter():
distance_from_tip = node.distance_from_tip()
if distance_from_tip > 0:
ages2.append(distance_from_tip)
ages2.sort()
for index in range(len(ages2)):
assert (ages[index] - ages2[index]) < 10e-6
pop_sizes2 = []
for edge in species_tree.postorder_edge_iter():
pop_sizes2.append(edge.pop_size)
pop_sizes2.sort()
return species_tree
def pop_gen_tree(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesim.pop_gen_tree()' function has moved to 'dendropy.simulate.popgensim.pop_gen_tree()'.",
old_construct="from dendropy import treesim\ntree = treesim.pop_gen_tree(...)",
new_construct="from dendropy.simulate import popgensim\ntree = popgensim.pop_gen_tree(...)",
)
return popgensim.pop_gen_tree(*args, **kwargs)
def pop_gen_tree(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.treesim.pop_gen_tree()' function has moved to 'dendropy.simulate.popgensim.pop_gen_tree()'.",
old_construct=
"from dendropy import treesim\ntree = treesim.pop_gen_tree(...)",
new_construct=
"from dendropy.simulate import popgensim\ntree = popgensim.pop_gen_tree(...)"
)
return popgensim.pop_gen_tree(*args, **kwargs)