def generateCoalescentTrees(choice, num, fout, length):
if choice == 1:
sp_tree_str = """\
[&R] ((((((((A,B)%d,C)%d,D)%d,E)%d,F)%d,G)%d,H)%d);
""" % (float(length),float(length),float(length),float(length),float(length),float(length),float(length))
elif choice == 2:
sp_tree_str = """\
[&R] ((((((((A,B)%d,C)%d,D)%d,E)%d,F)%d,G)%d,H)%d);
""" % (float(length),float(length),float(length),float(length),float(length),float(length),float(length))
sp_tree = dendropy.Tree.get_from_string(sp_tree_str, "newick")
gene_to_species_map = dendropy.TaxonNamespaceMapping.create_contained_taxon_mapping(
containing_taxon_namespace=sp_tree.taxon_namespace,
num_contained=1)
gene_tree_list = TreeList()
for i in range(num):
gene_tree = treesim.contained_coalescent_tree(containing_tree=sp_tree,
gene_to_containing_taxon_map=gene_to_species_map)
treesim.contained_coalescent_tree(containing_tree=sp_tree,
gene_to_containing_taxon_map=gene_to_species_map)
for t in gene_tree.leaf_nodes():
t.taxon.label = t.taxon.label.split( )[0]
gene_tree_list.append(gene_tree)
gene_tree_list.write_to_path(fout, 'newick')
def contained_coalescent(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesim.contained_coalescent()' function has moved to 'dendropy.simulate.treesim.contained_coalescent_tree()'.",
old_construct="from dendropy import treesim\ntree = treesim.contained_coalescent(...)",
new_construct="from dendropy.simulate import treesim\ntree = treesim.contained_coalescent_tree(...)",
)
return treesim.contained_coalescent_tree(*args, **kwargs)
def contained_coalescent(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.treesim.contained_coalescent()' function has moved to 'dendropy.simulate.treesim.contained_coalescent_tree()'.",
old_construct=
"from dendropy import treesim\ntree = treesim.contained_coalescent(...)",
new_construct=
"from dendropy.simulate import treesim\ntree = treesim.contained_coalescent_tree(...)"
)
return treesim.contained_coalescent_tree(*args, **kwargs)
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import dendropy
from dendropy.simulate import treesim
sp_tree_str = """\
[&R] (A:10,(B:6,(C:4,(D:2,E:2):2):2):4);
"""
sp_tree = dendropy.Tree.get(data=sp_tree_str, schema="newick")
gene_to_species_map = dendropy.TaxonNamespaceMapping.create_contained_taxon_mapping(
containing_taxon_namespace=sp_tree.taxon_namespace,
num_contained=3)
gene_tree = treesim.contained_coalescent_tree(containing_tree=sp_tree,
gene_to_containing_taxon_map=gene_to_species_map)
print(gene_tree.as_string(schema='newick'))
print(gene_tree.as_ascii_plot())
genes_to_species = dendropy.TaxonNamespaceMapping.create_contained_taxon_mapping(
containing_taxon_namespace=containing_taxa,
num_contained=8)
# convert to containing tree
stepwise_tree = reconcile.ContainingTree(stepwise_tree,
contained_taxon_namespace=genes_to_species.domain_taxon_namespace,
contained_to_containing_taxon_map=genes_to_species)
frag_tree = reconcile.ContainingTree(frag_tree,
contained_taxon_namespace=genes_to_species.domain_taxon_namespace,
contained_to_containing_taxon_map=genes_to_species)
# for each rep
for rep in range(num_reps):
gene_tree1 = treesim.contained_coalescent_tree(containing_tree=stepwise_tree,
gene_to_containing_taxon_map=genes_to_species,
default_pop_size=40000)
stepwise_tree.embed_tree(gene_tree1)
gene_tree2 = treesim.contained_coalescent_tree(containing_tree=frag_tree,
gene_to_containing_taxon_map=genes_to_species,
default_pop_size=40000)
frag_tree.embed_tree(gene_tree2)
# write results
# returns dictionary with contained trees as keys
# and number of deep coalescences as values
stepwise_deep_coals = stepwise_tree.deep_coalescences()
stepwise_out = open("stepwise.txt", "w")
for tree in stepwise_deep_coals:
stepwise_out.write("%d\n" % stepwise_deep_coals[tree])
#! /usr/bin/env python
import dendropy
from dendropy.simulate import treesim
sp_tree_str = """\
[&R] (A:10,(B:6,(C:4,(D:2,E:2):2):2):4);
"""
sp_tree = dendropy.Tree.get(data=sp_tree_str, schema="newick")
gene_to_species_map = dendropy.TaxonNamespaceMapping.create_contained_taxon_mapping(
containing_taxon_namespace=sp_tree.taxon_namespace,
num_contained=[
3,
4,
6,
2,
2,
])
gene_tree = treesim.contained_coalescent_tree(
containing_tree=sp_tree, gene_to_containing_taxon_map=gene_to_species_map)
print(gene_tree.as_string(schema='newick'))
print(gene_tree.as_ascii_plot())
#! /usr/bin/env python import sys import dendropy from dendropy.simulate import treesim species_tree_file_name = sys.argv[1] population_size = int(sys.argv[2]) sample_size = int(sys.argv[3]) species_tree = dendropy.Tree.get_from_path(species_tree_file_name, "nexus") gene_to_species_map = dendropy.TaxonNamespaceMapping.create_contained_taxon_mapping(containing_taxon_namespace=species_tree.taxon_namespace, num_contained=sample_size) gene_tree = treesim.contained_coalescent_tree(containing_tree=species_tree, gene_to_containing_taxon_map=gene_to_species_map, default_pop_size=population_size) print(gene_tree.as_string(schema='newick'))
# convert to containing tree
stepwise_tree = reconcile.ContainingTree(
stepwise_tree,
contained_taxon_namespace=genes_to_species.domain_taxon_namespace,
contained_to_containing_taxon_map=genes_to_species,
)
frag_tree = reconcile.ContainingTree(
frag_tree,
contained_taxon_namespace=genes_to_species.domain_taxon_namespace,
contained_to_containing_taxon_map=genes_to_species,
)
# for each rep
for rep in range(num_reps):
gene_tree1 = treesim.contained_coalescent_tree(
containing_tree=stepwise_tree, gene_to_containing_taxon_map=genes_to_species, default_pop_size=40000
)
stepwise_tree.embed_tree(gene_tree1)
gene_tree2 = treesim.contained_coalescent_tree(
containing_tree=frag_tree, gene_to_containing_taxon_map=genes_to_species, default_pop_size=40000
)
frag_tree.embed_tree(gene_tree2)
# write results
# returns dictionary with contained trees as keys
# and number of deep coalescences as values
stepwise_deep_coals = stepwise_tree.deep_coalescences()
stepwise_out = open("stepwise.txt", "w")
for tree in stepwise_deep_coals:
stepwise_out.write("%d\n" % stepwise_deep_coals[tree])