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