def get_species_tree(self, ntax=10):
_RNG = RepeatedRandom()
ages = [random.randint(1000,10000) for age in range(ntax)]
ages.sort()
pop_sizes = [random.randint(1000,10000) for pop in range(2*ntax+1)]
taxon_set = dendropy.new_taxon_set(ntax)
species_tree = treesim.pop_gen_tree(taxon_set=taxon_set,
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 = RepeatedRandom()
ages = [random.randint(1000, 10000) for age in range(ntax)]
ages.sort()
pop_sizes = [
random.randint(1000, 10000) for pop in range(2 * ntax + 1)
]
taxon_set = dendropy.new_taxon_set(ntax)
species_tree = treesim.pop_gen_tree(taxon_set=taxon_set,
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 runTest(self):
"""PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
_RNG = RepeatedRandom()
t = treesim.pure_kingman(dendropy.new_taxon_set(100), rng=_RNG)
assert t._debug_tree_is_valid()
def runTest(self):
"""PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
_RNG = RepeatedRandom()
t = treesim.pure_kingman(dendropy.new_taxon_set(100), rng=_RNG)
assert t._debug_tree_is_valid()