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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
import math
import unittest
import json
import dendropy
from dendropy.model import multispeciescoalescent
from dendropy.test.support import pathmap
def generate_multispecies_coalescent_system(
speciation_ages,
coalescent_ages,
):
"""
Generates a species tree and a coalescent tree based on Figure 1 of:
Rannala B, Yang Z. 2003. Bayesian estimation of species divergence
ages and ancestral population sizes using DNA sequences from
multiple loci. Genetics 164L 1645-1656.
"""
assert len(speciation_ages) == 3
assert len(coalescent_ages) == 6
speciation_ages = sorted(float(i) for i in speciation_ages)
coalescent_ages = sorted(float(i) for i in coalescent_ages)
species_taxa = dendropy.TaxonNamespace(["H","C","G","O"])
species_tree_str = "(((H,C)HC,G)HCG,O)HCGO;"
species_tree = dendropy.Tree.get(
data=species_tree_str,
schema="newick",
taxon_namespace=species_taxa,
rooting="force-rooted",
)
species_taxa.is_mutable = False
for nd in species_tree.leaf_node_iter():
nd.age = 0.0
nd.label = nd.taxon.label
species_tree.find_node_with_label("HC").age = speciation_ages[0]
species_tree.find_node_with_label("HCG").age = speciation_ages[1]
species_tree.find_node_with_label("HCGO").age = speciation_ages[2]
species_tree.set_edge_lengths_from_node_ages()
gene_taxa = dendropy.TaxonNamespace(["H1", "H2", "H3", "C1", "C2", "G", "O"])
coalescent_tree_str = "(((H1, ((H2, H3)a,(C1, C2)b)c)d,G)e,O)f;"
coalescent_tree = dendropy.Tree.get(
data=coalescent_tree_str,
schema="newick",
taxon_namespace=gene_taxa,
rooting="force-rooted",
)
gene_taxa.is_mutable = False
for nd in coalescent_tree.leaf_node_iter():
nd.age = 0.0
nd.label = nd.taxon.label
coalescent_tree.find_node_with_label("a").age = coalescent_ages[0]
coalescent_tree.find_node_with_label("b").age = coalescent_ages[1]
coalescent_tree.find_node_with_label("c").age = coalescent_ages[2]
coalescent_tree.find_node_with_label("d").age = coalescent_ages[3]
coalescent_tree.find_node_with_label("e").age = coalescent_ages[4]
coalescent_tree.find_node_with_label("f").age = coalescent_ages[5]
coalescent_tree.set_edge_lengths_from_node_ages()
coalescent_to_species_taxon_map = {
gene_taxa.require_taxon("H1"): species_taxa.require_taxon("H"),
gene_taxa.require_taxon("H2"): species_taxa.require_taxon("H"),
gene_taxa.require_taxon("H3"): species_taxa.require_taxon("H"),
gene_taxa.require_taxon("C1"): species_taxa.require_taxon("C"),
gene_taxa.require_taxon("C2"): species_taxa.require_taxon("C"),
gene_taxa.require_taxon("G"): species_taxa.require_taxon("G"),
gene_taxa.require_taxon("O"): species_taxa.require_taxon("O"),
}
return species_tree, coalescent_tree, coalescent_to_species_taxon_map
class MultispeciesCoalescentFixedSingleTreesCalculationTestCase(unittest.TestCase):
def test1(self):
with open(pathmap.other_source_path("multispecies_coalescent_test_data.json")) as src:
test_regimes = json.load(src)
for test_regime in test_regimes:
species_tree = dendropy.Tree.get(
data=test_regime["species_tree"],
schema="newick",
rooting="force-rooted",
)
species_tree.taxon_namespace.is_mutable = False
msc = multispeciescoalescent.MultispeciesCoalescent(species_tree=species_tree)
coalescent_species_lineage_label_map = test_regime["coalescent_species_lineage_label_map"]
coalescent_species_lineage_map_fn = lambda x: species_tree.taxon_namespace.require_taxon(coalescent_species_lineage_label_map[x.label])
coalescent_taxa = dendropy.TaxonNamespace(sorted(coalescent_species_lineage_label_map.keys()))
coalescent_taxa.is_mutable = False
for sub_regime in test_regime["coalescent_trees"]:
coalescent_tree = dendropy.Tree.get(
data=sub_regime["coalescent_tree"],
schema="newick",
rooting="force-rooted",
taxon_namespace=coalescent_taxa,
)
obs_ln_likelihood = msc.score_coalescent_tree(
coalescent_tree=coalescent_tree,
coalescent_species_lineage_map_fn=coalescent_species_lineage_map_fn,
)
exp_ln_likelihood = sub_regime["log_likelihood"]
self.assertAlmostEqual(obs_ln_likelihood, exp_ln_likelihood, 2)
class MultispeciesCoalescentBasicTestCase(unittest.TestCase):
def calc_log_likelihood(self,
species_tree,
coalescent_tree,
thetas=None,
default_theta=1.0,
):
tau_HC = species_tree.find_node_with_label("HC").age
tau_HCG = species_tree.find_node_with_label("HCG").age
tau_HCGO = species_tree.find_node_with_label("HCGO").age
t3_H = coalescent_tree.find_node_with_label("a").age
t2_C = coalescent_tree.find_node_with_label("b").age
t3_HC = coalescent_tree.find_node_with_label("c").age - species_tree.find_node_with_label("HC").age
t2_HC = coalescent_tree.find_node_with_label("d").age - coalescent_tree.find_node_with_label("c").age
t3_HCGO = coalescent_tree.find_node_with_label("e").age - species_tree.find_node_with_label("HCGO").age
t2_HCGO = coalescent_tree.find_node_with_label("f").age - coalescent_tree.find_node_with_label("e").age
if thetas is None:
thetas = {}
theta_H = thetas.get("H", default_theta)
theta_C = thetas.get("C", default_theta)
theta_HC = thetas.get("HC", default_theta)
theta_HCG = thetas.get("HCG", default_theta)
theta_HCGO = thetas.get("HCGO", default_theta)
p1 = 2.0/theta_H * math.exp(-6 * t3_H/theta_H) * math.exp(-2 * (tau_HC-t3_H)/theta_H)
p2 = 2.0/theta_C * math.exp(-2 * t2_C/theta_C)
p3 = 2.0/theta_HC * math.exp(-6 * t3_HC/theta_HC) * 2.0/theta_HC * math.exp(-2 * t2_HC/theta_HC)
# below is as originally given in the Rannala and Yang paper,
# but is incorrect
# p4 = math.exp(-2 * (tau_HCG - tau_HC - (t3_HC + t2_HC)) / theta_HCG)
p4 = math.exp(-2 * (tau_HCGO - tau_HCG) / theta_HCG)
p5 = 2.0/theta_HCGO * math.exp(-6 * t3_HCGO/theta_HCGO)
p6 = 2.0/theta_HCGO * math.exp(-2 * t2_HCGO/theta_HCGO)
p = p1 * p2 * p3 * p4 * p5 * p6
q1 = math.log(2.0/theta_H) + (-6 * t3_H/theta_H) + (-2 * (tau_HC-t3_H)/theta_H)
q2 = math.log(2.0/theta_C) + (-2 * t2_C/theta_C)
q3 = math.log(2.0/theta_HC) + (-6 * t3_HC/theta_HC) + math.log(2.0/theta_HC) + (-2 * t2_HC/theta_HC)
# below is as originally given in the Rannala and Yang paper,
# but is incorrect
# q4 = (-2 * (tau_HCG - tau_HC - (t3_HC + t2_HC)) / theta_HCG)
q4 = (-2 * (tau_HCGO - tau_HCG) / theta_HCG)
q5 = math.log(2.0/theta_HCGO) + (-6 * t3_HCGO/theta_HCGO)
q6 = math.log(2.0/theta_HCGO) + (-2 * t2_HCGO/theta_HCGO)
q = q1 + q2 + q3 + q4 + q5 + q6
self.assertAlmostEqual(math.log(p), q, 7)
return q
def get_node(self, tree, label):
return tree.find_node(filter_fn=lambda n: n.label==label)
def get_edge(self, tree, label):
return tree.find_node(filter_fn=lambda n: n.label==label).edge
def test_fixed_species_tree_fitting(self):
species_tree, coalescent_tree, coalescent_to_species_taxon_map = generate_multispecies_coalescent_system(
speciation_ages=[10, 20, 30],
coalescent_ages=[5, 6, 15, 16, 35, 36]
)
msc = multispeciescoalescent.MultispeciesCoalescent(species_tree)
edge_head_coalescent_edges, edge_tail_coalescent_edges, edge_coalescent_nodes = msc._fit_coalescent_tree(
coalescent_tree=coalescent_tree,
coalescent_species_lineage_map_fn=lambda x: coalescent_to_species_taxon_map[x])
expected_head_coalescent_edges = {
self.get_edge(species_tree, "H"): set([
self.get_edge(coalescent_tree, "H1"),
self.get_edge(coalescent_tree, "H2"),
self.get_edge(coalescent_tree, "H3"),
]),
self.get_edge(species_tree, "C"): set([
self.get_edge(coalescent_tree, "C1"),
self.get_edge(coalescent_tree, "C2"),
]),
self.get_edge(species_tree, "G"): set([
self.get_edge(coalescent_tree, "G"),
]),
self.get_edge(species_tree, "O"): set([
self.get_edge(coalescent_tree, "O"),
]),
self.get_edge(species_tree, "HC"): set([
self.get_edge(coalescent_tree, "H1"),
self.get_edge(coalescent_tree, "a"),
self.get_edge(coalescent_tree, "b"),
]),
self.get_edge(species_tree, "HCG"): set([
self.get_edge(coalescent_tree, "d"),
self.get_edge(coalescent_tree, "G"),
]),
self.get_edge(species_tree, "HCGO"): set([
self.get_edge(coalescent_tree, "d"),
self.get_edge(coalescent_tree, "G"),
self.get_edge(coalescent_tree, "O"),
]),
}
expected_tail_coalescent_edges = {
self.get_edge(species_tree, "H"): set([
self.get_edge(coalescent_tree, "H1"),
self.get_edge(coalescent_tree, "a"),
]),
self.get_edge(species_tree, "C"): set([
self.get_edge(coalescent_tree, "b"),
]),
self.get_edge(species_tree, "G"): set([
self.get_edge(coalescent_tree, "G"),
]),
self.get_edge(species_tree, "O"): set([
self.get_edge(coalescent_tree, "O"),
]),
self.get_edge(species_tree, "HC"): set([
self.get_edge(coalescent_tree, "d"),
]),
self.get_edge(species_tree, "HCG"): set([
self.get_edge(coalescent_tree, "d"),
self.get_edge(coalescent_tree, "G"),
]),
self.get_edge(species_tree, "HCGO"): set([
]),
}
expected_coalescing_nodes = {
self.get_edge(species_tree, "H"): set([
self.get_node(coalescent_tree, "a"),
]),
self.get_edge(species_tree, "C"): set([
self.get_node(coalescent_tree, "b"),
]),
self.get_edge(species_tree, "G"): set([
]),
self.get_edge(species_tree, "O"): set([
]),
self.get_edge(species_tree, "HC"): set([
self.get_node(coalescent_tree, "d"),
self.get_node(coalescent_tree, "c"),
]),
self.get_edge(species_tree, "HCG"): set([
]),
self.get_edge(species_tree, "HCGO"): set([
self.get_node(coalescent_tree, "f"),
self.get_node(coalescent_tree, "e"),
]),
}
for species_tree_edge in edge_head_coalescent_edges:
# print("-- {} --".format(species_tree_edge.head_node.label if species_tree_edge.head_node else "<root>"))
# print("{}: {} vs. {}".format(
# species_tree_edge.head_node.label,
# [ce.head_node.label for ce in edge_head_coalescent_edges[species_tree_edge]],
# [ce.head_node.label for ce in expected_head_coalescent_edges[species_tree_edge]]))
self.assertEqual(
set(edge_head_coalescent_edges[species_tree_edge]),
expected_head_coalescent_edges[species_tree_edge]
)
# print("{}: {} vs. {}".format(
# species_tree_edge.head_node.label if species_tree_edge.head_node else "<root>",
# [ce.head_node.label for ce in edge_tail_coalescent_edges[species_tree_edge]],
# [ce.head_node.label for ce in expected_tail_coalescent_edges[species_tree_edge]]))
self.assertEqual(
set(edge_tail_coalescent_edges[species_tree_edge]),
expected_tail_coalescent_edges[species_tree_edge]
)
# print("{}: {} vs. {}".format(
# species_tree_edge.head_node.label if species_tree_edge.head_node else "<root>",
# [nd.label for nd in edge_coalescent_nodes[species_tree_edge]],
# [nd.label for nd in expected_coalescing_nodes[species_tree_edge]]))
self.assertEqual(
set(edge_coalescent_nodes[species_tree_edge]),
expected_coalescing_nodes[species_tree_edge]
)
expected_lnL = self.calc_log_likelihood(
species_tree=species_tree,
coalescent_tree=coalescent_tree,)
s = msc.score_coalescent_tree(
coalescent_tree=coalescent_tree,
coalescent_species_lineage_map_fn=lambda x: coalescent_to_species_taxon_map[x],
)
self.assertAlmostEqual(s, expected_lnL)
if __name__ == "__main__":
unittest.main()
|
