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)