def reconciliation_discordance(gene_tree, species_tree):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct="from dendropy import reconcile\nreconcile.reconciliation_discordance(...)",
new_construct="from dendropy.model import reconcile\nreconcile.reconciliation_discordance(...)",
)
return reconcile.reconciliation_discordance(gene_tree, species_tree)
def reconciliation_discordance(gene_tree, species_tree):
deprecate.dendropy_deprecation_warning(
preamble=
"The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct=
"from dendropy import reconcile\nreconcile.reconciliation_discordance(...)",
new_construct=
"from dendropy.model import reconcile\nreconcile.reconciliation_discordance(...)",
)
return reconcile.reconciliation_discordance(gene_tree, species_tree)
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 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
