#! /usr/bin/env python
import dendropy
from dendropy import treesim
sp_tree_str = """\
[&R] (A:10,(B:6,(C:4,(D:2,E:2):2):2):4)
"""
sp_tree = dendropy.Tree.get_from_string(sp_tree_str, "newick")
gene_to_species_map = dendropy.TaxonSetMapping.create_contained_taxon_mapping(
containing_taxon_set=sp_tree.taxon_set, num_contained=3)
gene_tree = treesim.contained_coalescent(
containing_tree=sp_tree, gene_to_containing_taxon_map=gene_to_species_map)
print(gene_tree.as_string('newick'))
print(gene_tree.as_ascii_plot())
#! /usr/bin/env python
import dendropy
from dendropy import treesim
sp_tree_str = """\
[&R] (A:10,(B:6,(C:4,(D:2,E:2):2):2):4)
"""
sp_tree = dendropy.Tree.get_from_string(sp_tree_str, "newick")
gene_to_species_map = dendropy.TaxonSetMapping.create_contained_taxon_mapping(
containing_taxon_set=sp_tree.taxon_set, num_contained=3
)
gene_tree = treesim.contained_coalescent(containing_tree=sp_tree, gene_to_containing_taxon_map=gene_to_species_map)
print(gene_tree.as_string("newick"))
print(gene_tree.as_ascii_plot())
"returns labels from taxon x"
return x.label
##comand line parsing
parser = optparse.OptionParser()
parser.add_option("-n", "--pop-size", type="float", help="effective population size, N_e", metavar="NUMBER",default=1e4)
parser.add_option("-N", "--number-trees", type="int", help="number of trees to generate for each species tree", metavar="NUMBER",default=100)
parser.add_option("-o", "--output-file", help="output coalescent trees to FILE", metavar="FILE")
parser.add_option("-s", "--species-file", help="read species trees from FILE", metavar="FILE", default="species.nex")
(options,args) = parser.parse_args()
if options.output_file==None:
genehandle = sys.stdout
else:
genehandle = open(options.output_file,"w")
species = dendropy.TreeList.get_from_path(options.species_file,"nexus",as_rooted=True)
taxon_map = dendropy.TaxonSetMapping.create_contained_taxon_mapping(species.taxon_set, 1,contained_taxon_label_func=mylabel)
tlist = dendropy.TreeList()
for tree in species:
for i in range(0,options.number_trees):
gene_tree = treesim.contained_coalescent(tree,taxon_map,default_pop_size=options.pop_size)
tlist.append(gene_tree)
##gene_tree.write_to_stream(genehandle,"newick",suppress_rooting=True)
tlist.write_to_stream(genehandle,"newick",suppress_rooting=True)
genehandle.close()
genes_to_species = dendropy.TaxonSetMapping.create_contained_taxon_mapping(
containing_taxon_set=containing_taxa,
num_contained=8)
# convert to containing tree
stepwise_tree = reconcile.ContainingTree(stepwise_tree,
embedded_taxon_set=genes_to_species.domain_taxon_set,
embedded_to_containing_taxon_map=genes_to_species)
frag_tree = reconcile.ContainingTree(frag_tree,
embedded_taxon_set=genes_to_species.domain_taxon_set,
embedded_to_containing_taxon_map=genes_to_species)
# for each rep
for rep in range(num_reps):
gene_tree1 = treesim.contained_coalescent(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(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 embedded 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])
containing_taxon_set=containing_taxa, num_contained=8)
# convert to containing tree
stepwise_tree = reconcile.ContainingTree(
stepwise_tree,
contained_taxon_set=genes_to_species.domain_taxon_set,
contained_to_containing_taxon_map=genes_to_species)
frag_tree = reconcile.ContainingTree(
frag_tree,
contained_taxon_set=genes_to_species.domain_taxon_set,
contained_to_containing_taxon_map=genes_to_species)
# for each rep
for rep in range(num_reps):
gene_tree1 = treesim.contained_coalescent(
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(
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: