#! /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())
Esempio n. 2
0
#! /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())
Esempio n. 3
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    "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: