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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 Tree taxon management
"""
import os
import unittest
import dendropy
import collections
import copy
from dendropy.test.support import curated_test_tree
from dendropy.test.support import compare_and_validate
from dendropy.test.support import dendropytest
class TestTreeUpdateTaxonNamespace(
curated_test_tree.CuratedTestTree,
dendropytest.ExtendedTestCase):
def setUp(self):
self.tree1, self.anodes1, self.lnodes1, self.inodes1 = self.get_tree(
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=True)
self.expected_labels = set([nd.label for nd in self.anodes1 if nd.label is not None])
self.expected_taxa = set()
for nd in self.tree1:
if nd.label is not None:
nd.taxon = dendropy.Taxon(label=nd.label)
self.expected_taxa.add(nd.taxon)
assert len(self.expected_labels) == len(self.anodes1)
assert len(self.expected_taxa) == len(self.expected_labels)
def test_noop_update_with_no_taxa(self):
tree, anodes, lnodes, inodes = self.get_tree(
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=True)
original_tns = tree.taxon_namespace
self.assertEqual(len(original_tns), 0)
tree.update_taxon_namespace()
self.assertIs(tree.taxon_namespace, original_tns)
self.assertEqual(len(original_tns), 0)
def test_noop_update(self):
tree, anodes, lnodes, inodes = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
original_tns = tree.taxon_namespace
original_taxa = [t for t in original_tns]
original_labels = [t.label for t in original_tns]
tree.update_taxon_namespace()
self.assertIs(tree.taxon_namespace, original_tns)
new_taxa = [t for t in original_tns]
new_labels = [t.label for t in original_tns]
self.assertEqual(new_taxa, original_taxa)
self.assertEqual(new_labels, original_labels)
def test_update_taxon_namespace(self):
tns1 = self.tree1.taxon_namespace
self.assertEqual(len(tns1), 0)
tns2 = self.tree1.update_taxon_namespace()
self.assertIs(self.tree1.taxon_namespace, tns1)
self.assertEqual(set(tns2._taxa), self.expected_taxa)
self.assertEqual(len(tns2._taxa), len(self.expected_labels))
class TestTreeMigrateAndReconstructTaxonNamespace(
curated_test_tree.CuratedTestTree,
dendropytest.ExtendedTestCase):
def setUp(self):
self.tree, self.anodes, self.lnodes, self.inodes = self.get_tree(
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=True)
self.node_label_to_taxon_label_map = {
"a" : "a",
"b" : "a",
"c" : "2",
"e" : "2",
"f" : "b",
"g" : "B",
"h" : "B",
"i" : "h",
"j" : "H",
"k" : "h",
"l" : None,
"m" : None,
"n" : "H",
"o" : "J",
"p" : "j",
}
self.original_taxa = []
for idx, nd in enumerate(self.tree):
taxon_label = self.node_label_to_taxon_label_map[nd.label]
t = dendropy.Taxon(label=taxon_label)
self.tree.taxon_namespace.add_taxon(t)
nd.taxon = t
nd.original_taxon = t
self.original_taxa.append(t)
assert len(self.tree.taxon_namespace) == len(self.node_label_to_taxon_label_map)
assert len(self.tree.taxon_namespace) == len(self.original_taxa)
def create_redundant_taxa(self):
nodes_to_unify_taxa = []
for nd in self.tree:
if nd.taxon.label and nd.taxon.label.upper() == "J":
nodes_to_unify_taxa.append(nd)
assert len(nodes_to_unify_taxa) >= 2
utaxon = nodes_to_unify_taxa[0].taxon
utaxon.node_label = nodes_to_unify_taxa[0].label
for nd in nodes_to_unify_taxa[1:]:
self.tree.taxon_namespace.remove_taxon(nd.taxon)
self.original_taxa.remove(nd.taxon)
nd.original_taxon = utaxon
nd.taxon = utaxon
del self.node_label_to_taxon_label_map[nd.label]
nd.label = utaxon.node_label
def verify_taxon_namespace_reconstruction(self,
unify_taxa_by_label=False,
case_sensitive_label_mapping=True,
original_tns=None,
redundant_taxa=False):
seen_taxa = []
if unify_taxa_by_label:
if not case_sensitive_label_mapping:
expected_labels = []
for label in self.node_label_to_taxon_label_map.values():
if label is None:
expected_labels.append(label)
else:
label = label.upper()
if label not in expected_labels:
expected_labels.append(label)
else:
expected_labels = list(set(label for label in self.node_label_to_taxon_label_map.values()))
else:
expected_labels = [label for label in self.node_label_to_taxon_label_map.values()]
for nd in self.tree:
self.assertIsNot(nd.taxon, nd.original_taxon)
if (not case_sensitive_label_mapping) and nd.taxon.label is not None:
self.assertEqual(nd.taxon.label.upper(), nd.original_taxon.label.upper())
self.assertEqual(self.node_label_to_taxon_label_map[nd.label].upper(), nd.taxon.label.upper())
else:
self.assertEqual(nd.taxon.label, nd.original_taxon.label)
self.assertEqual(self.node_label_to_taxon_label_map[nd.label], nd.taxon.label)
self.assertNotIn(nd.original_taxon, self.tree.taxon_namespace)
self.assertIn(nd.original_taxon, self.original_taxa)
self.assertIn(nd.taxon, self.tree.taxon_namespace)
self.assertNotIn(nd.taxon, self.original_taxa)
if original_tns is not None:
self.assertNotIn(nd.taxon, original_tns)
if nd.taxon not in seen_taxa:
seen_taxa.append(nd.taxon)
else:
self.assertTrue(unify_taxa_by_label or redundant_taxa)
if not case_sensitive_label_mapping:
self.assertIn(nd.taxon.label, [t.label for t in seen_taxa])
else:
if nd.taxon.label is None:
self.assertIs(nd.original_taxon.label, None)
self.assertEqual([t.label for t in seen_taxa].count(None), 1)
else:
x1 = [t.label.upper() for t in seen_taxa if t.label is not None]
self.assertIn(nd.taxon.label.upper(), x1)
self.assertEqual(len(self.tree.taxon_namespace), len(expected_labels))
if not unify_taxa_by_label and not redundant_taxa:
self.assertEqual(len(self.tree.taxon_namespace), len(self.node_label_to_taxon_label_map))
self.assertEqual(len(seen_taxa), len(self.tree.taxon_namespace))
if not case_sensitive_label_mapping:
seen_labels = [(t.label.upper() if t.label is not None else None) for t in seen_taxa]
else:
seen_labels = [t.label for t in seen_taxa]
c1 = collections.Counter(expected_labels)
c2 = collections.Counter(seen_labels)
self.assertEqual(c1, c2)
def test_noop_taxon_namespace_reconstruction(self):
tree, anodes, lnodes, inodes = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
original_tns = tree.taxon_namespace
original_tns.is_case_sensitive = True
original_taxa = [t for t in original_tns]
original_labels = [t.label for t in original_tns]
tree.reconstruct_taxon_namespace(
unify_taxa_by_label=False)
self.assertIs(tree.taxon_namespace, original_tns)
new_taxa = [t for t in original_tns]
new_labels = [t.label for t in original_tns]
self.assertEqual(new_taxa, original_taxa)
self.assertEqual(new_labels, original_labels)
def test_reconstruct_taxon_namespace_non_unifying(self):
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = True
self.tree._taxon_namespace = new_tns
self.assertEqual(len(self.tree.taxon_namespace), 0)
self.tree.reconstruct_taxon_namespace(unify_taxa_by_label=False)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
self.verify_taxon_namespace_reconstruction(
unify_taxa_by_label=False,
case_sensitive_label_mapping=True)
def test_reconstruct_taxon_namespace_unifying_case_sensitive(self):
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = True
self.tree._taxon_namespace = new_tns
self.assertEqual(len(self.tree.taxon_namespace), 0)
self.tree.reconstruct_taxon_namespace(unify_taxa_by_label=True)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
self.verify_taxon_namespace_reconstruction(
unify_taxa_by_label=True,
case_sensitive_label_mapping=True,
original_tns=original_tns)
def test_reconstruct_taxon_namespace_unifying_case_insensitive(self):
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = False
self.tree._taxon_namespace = new_tns
self.assertEqual(len(self.tree.taxon_namespace), 0)
self.tree.reconstruct_taxon_namespace(unify_taxa_by_label=True)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
self.verify_taxon_namespace_reconstruction(
unify_taxa_by_label=True,
case_sensitive_label_mapping=False,
original_tns=original_tns)
def test_reconstruct_taxon_namespace_with_redundant_taxa(self):
for (unify, ci) in [
(False, True),
(True, True),
(True, False), ]:
self.setUp()
self.create_redundant_taxa()
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = ci
self.tree._taxon_namespace = new_tns
self.assertEqual(len(self.tree.taxon_namespace), 0)
self.tree.reconstruct_taxon_namespace(unify_taxa_by_label=unify)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
self.verify_taxon_namespace_reconstruction(
unify_taxa_by_label=unify,
case_sensitive_label_mapping=ci,
original_tns=original_tns,
redundant_taxa=True)
def test_reconstruct_taxon_namespace_mapping(self):
for (unify, ci) in [
(False, False),
(True, False),
(True, True), ]:
self.setUp()
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = ci
self.tree._taxon_namespace = new_tns
self.assertEqual(len(self.tree.taxon_namespace), 0)
memo = {}
for taxon in self.original_taxa:
memo[taxon] = dendropy.Taxon()
memo_copy = dict(memo)
self.tree.reconstruct_taxon_namespace(
unify_taxa_by_label=unify,
taxon_mapping_memo=memo)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
for nd in self.tree:
self.assertIs(nd.taxon, memo_copy[nd.original_taxon])
def test_noop_migrate_taxon_namespace(self):
tree, anodes, lnodes, inodes = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
original_tns = tree.taxon_namespace
original_tns.is_case_sensitive = True
original_taxa = [t for t in original_tns]
original_labels = [t.label for t in original_tns]
tree.migrate_taxon_namespace(
original_tns,
unify_taxa_by_label=False)
self.assertIs(tree.taxon_namespace, original_tns)
new_taxa = [t for t in original_tns]
new_labels = [t.label for t in original_tns]
self.assertEqual(new_taxa, original_taxa)
self.assertEqual(new_labels, original_labels)
def test_simple_migrate_taxon_namespace(self):
tree, anodes, lnodes, inodes = self.get_tree(
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=True)
original_tns = tree.taxon_namespace
original_taxa = [t for t in original_tns]
original_labels = [t.label for t in original_tns]
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = True
tree.migrate_taxon_namespace(
new_tns,
unify_taxa_by_label=False)
self.assertIsNot(tree.taxon_namespace, original_tns)
self.assertIs(tree.taxon_namespace, new_tns)
new_taxa = [t for t in new_tns]
self.assertEqual(len(new_taxa), len(original_taxa))
for t1, t2 in zip(new_taxa, original_taxa):
self.assertIsNot(t1, t2)
self.assertEqual(t1.label, t2.label)
def test_migrate_taxon_namespace_non_unifying(self):
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = True
self.tree.migrate_taxon_namespace(
new_tns,
unify_taxa_by_label=False)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
self.verify_taxon_namespace_reconstruction(
unify_taxa_by_label=False,
case_sensitive_label_mapping=True,
original_tns=original_tns)
def test_migrate_taxon_namespace_unifying_case_sensitive(self):
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = True
self.tree.migrate_taxon_namespace(
new_tns,
unify_taxa_by_label=True)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
self.verify_taxon_namespace_reconstruction(
unify_taxa_by_label=True,
case_sensitive_label_mapping=True,
original_tns=original_tns)
def test_migrate_taxon_namespace_unifying_case_insensitive(self):
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = False
self.tree.migrate_taxon_namespace(
new_tns,
unify_taxa_by_label=True)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
self.verify_taxon_namespace_reconstruction(
unify_taxa_by_label=True,
case_sensitive_label_mapping=False,
original_tns=original_tns)
def test_migrate_taxon_namespace_mapping(self):
for (unify, ci) in [
(False, True),
(True, True),
(True, False), ]:
self.setUp()
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = ci
memo = {}
for taxon in self.original_taxa:
memo[taxon] = dendropy.Taxon()
memo_copy = dict(memo)
self.tree.migrate_taxon_namespace(
new_tns,
unify_taxa_by_label=unify,
taxon_mapping_memo=memo)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
for nd in self.tree:
self.assertIs(nd.taxon, memo_copy[nd.original_taxon])
def test_migrate_taxon_namespace_with_redundant_taxa(self):
for (unify, ci) in [
(False, True),
(True, True),
(True, False), ]:
self.setUp()
self.create_redundant_taxa()
original_tns = self.tree.taxon_namespace
new_tns = dendropy.TaxonNamespace()
new_tns.is_case_sensitive = ci
self.tree.migrate_taxon_namespace(
new_tns,
unify_taxa_by_label=unify)
self.assertIsNot(self.tree.taxon_namespace, original_tns)
self.assertIs(self.tree.taxon_namespace, new_tns)
self.verify_taxon_namespace_reconstruction(
unify_taxa_by_label=unify,
case_sensitive_label_mapping=ci,
original_tns=original_tns,
redundant_taxa=True)
def test_unassign_taxa(self):
self.assertFalse(self.fail_incomplete_tests())
def test_randomly_assign_taxa(self):
self.assertFalse(self.fail_incomplete_tests())
class TestTreeTaxa(
curated_test_tree.CuratedTestTree,
dendropytest.ExtendedTestCase):
def setUp(self):
self.tree1, self.anodes1, self.lnodes1, self.inodes1 = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
self.expected_taxa = set([nd.taxon for nd in self.anodes1 if nd.taxon is not None])
def test_basic_taxa(self):
self.assertEqual(self.tree1.poll_taxa(), self.expected_taxa)
class TestTreePurgeTaxonNamespace(
curated_test_tree.CuratedTestTree,
dendropytest.ExtendedTestCase):
def setUp(self):
self.tree1, self.anodes1, self.lnodes1, self.inodes1 = self.get_tree(
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
self.expected_taxa = set([nd.taxon for nd in self.anodes1 if nd.taxon is not None])
def test_noop_purge(self):
self.assertEqual(set(self.tree1.taxon_namespace), self.expected_taxa)
self.tree1.purge_taxon_namespace()
self.assertEqual(set(self.tree1.taxon_namespace), self.expected_taxa)
def test_basic_purge(self):
self.assertEqual(set(self.tree1.taxon_namespace), self.expected_taxa)
added_taxa = set(self.expected_taxa)
for label in ("z1", "z2", "z3", "z4"):
t = self.tree1.taxon_namespace.new_taxon(label=label)
added_taxa.add(t)
self.assertEqual(set(self.tree1.taxon_namespace), added_taxa)
self.tree1.purge_taxon_namespace()
self.assertEqual(set(self.tree1.taxon_namespace), self.expected_taxa)
if __name__ == "__main__":
unittest.main()
|
