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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.
##
##############################################################################
"""
Tests reconciliation calculations.
"""
import os
import unittest
import dendropy
from dendropy.test.support import pathmap
from dendropy.utility.messaging import get_logger
_LOG = get_logger(__name__)
from dendropy.model import reconcile
class ContainingTreeDeepCoalescenceSmall(unittest.TestCase):
def setUp(self):
dataset = dendropy.DataSet.get_from_path(pathmap.tree_source_path(filename="deepcoal1.nex"), "nexus")
self.species_tree = dataset.get_tree_list(label="ContainingTree")[0]
self.gene_trees = dataset.get_tree_list(label="EmbeddedTrees")
self.species_tree.taxon_namespace.is_mutable = False
self.gene_taxon_to_population_taxon_map = dendropy.TaxonNamespaceMapping(
domain_taxon_namespace=self.gene_trees.taxon_namespace,
range_taxon_namespace=self.species_tree.taxon_namespace,
mapping_fn=lambda t: self.species_tree.taxon_namespace.require_taxon(label=t.label[0].upper()))
self.expected_under_original_brlens = [4, 6, 4, 2, 4, 3, 3, 4, 5, 4]
def testFixedEdgesDeepCoalCount(self):
results = []
for idx, gt in enumerate(self.gene_trees):
ct = reconcile.ContainingTree(containing_tree=self.species_tree,
contained_taxon_namespace=self.gene_trees.taxon_namespace,
contained_to_containing_taxon_map=self.gene_taxon_to_population_taxon_map,
contained_trees=[gt],
fit_containing_edge_lengths=False,
)
dc = ct.num_deep_coalescences()
results.append(dc)
## FOR DEBUGGING
# mesqf = pathmap.named_output_stream("ContainingTreeDeepCoalescence_Small_FixedEdges_t%02d_dc%02d.nex" % (idx+1, dc), False)
# with mesqf:
# ct.write_as_mesquite(mesqf)
self.assertEqual(results, self.expected_under_original_brlens)
def testFittedEdgesDeepCoalCount(self):
for idx, gt in enumerate(self.gene_trees):
gt.encode_bipartitions()
ct = reconcile.ContainingTree(containing_tree=self.species_tree,
contained_taxon_namespace=self.gene_trees.taxon_namespace,
contained_to_containing_taxon_map=self.gene_taxon_to_population_taxon_map,
contained_trees=[gt],
fit_containing_edge_lengths=True,
)
dc = ct.num_deep_coalescences()
## FOR DEBUGGING
# mesqf = pathmap.named_output_stream("ContainingTreeDeepCoalescence_Small_FittedEdges_t%02d_dc%02d.nex" % (idx+1, dc), False)
# with mesqf:
# ct.write_as_mesquite(mesqf)
class DeepCoalTest(unittest.TestCase):
def testFittedDeepCoalCounting(self):
taxa = dendropy.TaxonNamespace()
gene_trees = dendropy.TreeList.get_from_string("""
[&R] (A,(B,(C,D))); [&R] ((A,C),(B,D)); [&R] (C,(A,(B,D)));
""", "newick", taxon_namespace=taxa)
species_trees = dendropy.TreeList.get_from_string("""
[&R] (A,(B,(C,D)));
[&R] (A,(C,(B,D)));
[&R] (A,(D,(C,B)));
[&R] (B,(A,(C,D)));
[&R] (B,(C,(A,D)));
[&R] (B,(D,(C,A)));
[&R] (C,(A,(B,D)));
[&R] (C,(B,(A,D)));
[&R] (C,(D,(B,A)));
[&R] (D,(A,(B,C)));
[&R] (D,(B,(A,C)));
[&R] (D,(C,(B,A)));
[&R] ((A,B),(C,D));
[&R] ((A,C),(B,D));
[&R] ((A,D),(C,B));
""", "NEWICK", taxon_namespace=taxa)
# expected results, for each gene tree / species tree pairing, with
# cycling through species trees for each gene tree
expected_deep_coalescences = [ 0, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 2, 2,
2, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 2, 2, 0, 2,
2, 1, 2, 3, 3, 3, 0, 1, 1, 3, 3, 3, 2, 1, 2 ]
assert len(expected_deep_coalescences) == len(gene_trees) * len(species_trees)
for t in gene_trees + species_trees:
t.update_bipartitions()
idx = 0
_LOG.info("Species\t\tGene\t\tDC\t\tExp.DC\t\tDiff")
for gt in gene_trees:
gt.update_bipartitions()
for st in species_trees:
st.update_bipartitions()
dc = reconcile.reconciliation_discordance(gt, st)
_LOG.info("%s\t\t%s\t\t%s\t\t%s\t\t%s"
% (st._as_newick_string(),
gt._as_newick_string(),
dc,
expected_deep_coalescences[idx],
dc - expected_deep_coalescences[idx]))
assert dc == expected_deep_coalescences[idx]
idx += 1
def testGroupedDeepCoalCounting(self):
src_trees = [
"((a1,a2)x,b1)y;",
"((a1, (a2, a3), b1), (b2,(b3,b4)));",
"(((((a1, a2),a3), b1), b2), (b3, ((b4,b5),b6)));",
"((b1, (b2, b3), a1), (a2,(a3, a4)));",
"(((((b1, b2),b3), a1), a2), (a3, ((a4,a5),a6)));",
"((a1,a2),(b1,b2),(c1,c2));",
"((a1,a2),(b1,b2,c3),(c1,c2));",
"(((a1,a2),(b1,b2),c1),c2);",
]
scores = [ 0, 1, 2, 1, 2, 0, 1, 1 ]
for src_tree, expected in zip(src_trees, scores):
tree = dendropy.Tree.get_from_string(src_tree, "NEWICK")
groups = dendropy.TaxonNamespacePartition(tree.taxon_namespace,
membership_fn=lambda x: x.label[0])
dc = reconcile.monophyletic_partition_discordance(tree, groups)
assert dc == expected, \
"deep coalescences by groups: expecting %d, but found %d" % (expected, dc)
if __name__ == "__main__":
unittest.main()
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