def runTest(self, ntax=10):
"""TruncatedCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
species_tree = self.get_species_tree(ntax)
gene_trees = []
while len(gene_trees) < 20:
gene_trees.append(
coalescent.constrained_kingman_tree(species_tree)[0])
def generate_gene_tree(self, species_name, samples_per_pop=10):
"""
Given:
``species_name`` : string identifying species/taxon
``samples_per_pop`` : number of samples (genes) per population
Returns:
DendroPy tree, with branch lengths in generations
"""
if self.pop_tree is None:
self.generate_pop_tree(species_name, samples_per_pop=10)
for idx, leaf in enumerate(self.pop_tree.leaf_iter()):
if idx == 1:
# ancestral population = num_desc_pops * desc population
leaf.parent_node.edge.pop_size = self.num_desc_pops * self.desc_pop_size
leaf.edge.pop_size = self.desc_pop_size
leaf.num_genes = samples_per_pop
self.gene_tree, self.pop_tree = coalescent.constrained_kingman_tree(
self.pop_tree,
gene_node_label_fn=lambda x, y: "%sX%d" % (x, y),
rng=self.rng)
self.mutation_tree = copy.deepcopy(self.gene_tree)
for edge in self.mutation_tree.preorder_edge_iter():
edge.length = edge.length * self.mutrate_per_site_per_generation
return self.gene_tree
def generate_gene_tree(self, species_name, samples_per_pop=10):
"""
Given:
``species_name`` : string identifying species/taxon
``samples_per_pop`` : number of samples (genes) per population
Returns:
DendroPy tree, with branch lengths in generations
"""
if self.pop_tree is None:
self.generate_pop_tree(species_name, samples_per_pop=10)
for idx, leaf in enumerate(self.pop_tree.leaf_iter()):
if idx == 1:
# ancestral population = num_desc_pops * desc population
leaf.parent_node.edge.pop_size = self.num_desc_pops * self.desc_pop_size
leaf.edge.pop_size = self.desc_pop_size
leaf.num_genes = samples_per_pop
self.gene_tree, self.pop_tree = coalescent.constrained_kingman_tree(self.pop_tree,
gene_node_label_fn=lambda x,y: "%sX%d" % (x,y),
rng=self.rng)
self.mutation_tree = copy.deepcopy(self.gene_tree)
for edge in self.mutation_tree.preorder_edge_iter():
edge.length = edge.length * self.mutrate_per_site_per_generation
return self.gene_tree
def runTest(self, ntax=10):
"""TruncatedCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
species_tree = self.get_species_tree(ntax)
gene_trees = []
while len(gene_trees) < 20:
gene_trees.append(coalescent.constrained_kingman_tree(species_tree)[0])