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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 for general NEWICK tree list reading.
"""
import sys
import unittest
import dendropy
from dendropy.test.support import dendropytest
from dendropy.test.support import standard_file_test_trees
from dendropy.test.support import curated_test_tree
from dendropy.test.support import pathmap
from dendropy.test import base_newick_test_cases
from dendropy.test import base_standard_trees_parsing_test_cases
if not (sys.version_info.major >= 3 and sys.version_info.minor >= 4):
from dendropy.utility.filesys import pre_py34_open as open
class NewickTreeListReaderDefaultTestCase(
base_standard_trees_parsing_test_cases.StandardTreesParsingTestCase,
standard_file_test_trees.NewickTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NewickTestTreesChecker.create_class_fixtures(cls)
# ## NOTE: tests are in base_standard_trees_parsing_test_cases.StandardTreesParsingTestCase, !! ##
class NewickTreeListReaderSuppressedInternalSuppressedLeafTaxaTestCase(
base_newick_test_cases.NewickTreeListReaderTaxaManagementBaseTestCase,
standard_file_test_trees.NewickTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NewickTestTreesChecker.create_class_fixtures(cls,
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=True,
)
class NewickTreeListReaderUnsuppressedInternalSuppressedLeafTaxaTestCase(
base_newick_test_cases.NewickTreeListReaderTaxaManagementBaseTestCase,
standard_file_test_trees.NewickTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NewickTestTreesChecker.create_class_fixtures(cls,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=True,
)
class NewickTreeListReaderSuppressedInternalUnsuppressedLeafTaxaTestCase(
base_newick_test_cases.NewickTreeListReaderTaxaManagementBaseTestCase,
standard_file_test_trees.NewickTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NewickTestTreesChecker.create_class_fixtures(cls,
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=False,
)
class NewickTreeListReaderUnsuppressedInternalUnsuppressedLeafTaxaTestCase(
base_newick_test_cases.NewickTreeListReaderTaxaManagementBaseTestCase,
standard_file_test_trees.NewickTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NewickTestTreesChecker.create_class_fixtures(cls,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False,
)
class NewickTreeListMetadataTest(
base_newick_test_cases.NewickTreeListReaderTaxaManagementBaseTestCase,
standard_file_test_trees.NewickTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NewickTestTreesChecker.create_class_fixtures(cls,
is_metadata_extracted=True,
)
def test_read_metadata(self):
tree_file_titles = [
"dendropy-test-trees-multifurcating-rooted-annotated",
"dendropy-test-trees-n33-unrooted-annotated-x10a",
]
for tree_file_title in tree_file_titles:
tree_filepath = standard_file_test_trees._TREE_FILEPATHS["newick"][tree_file_title]
with open(tree_filepath, "r") as src:
tree_string = src.read()
with open(tree_filepath, "r") as tree_stream:
approaches = (
(dendropy.TreeList.get_from_path, tree_filepath),
(dendropy.TreeList.get_from_stream, tree_stream),
(dendropy.TreeList.get_from_string, tree_string),
)
for method, src in approaches:
tree_list = method(src,
"newick",
extract_comment_metadata=True)
self.verify_standard_trees(
tree_list=tree_list,
tree_file_title=tree_file_title)
class NewickTreeListRootingAndMetadataTest(
standard_file_test_trees.StandardTestTreesChecker,
dendropytest.ExtendedTestCase):
def test_correct_rooting_weighting_and_metadata_association(self):
tree_str = """\
;;;;
[&color=red][&W 0.25][&R](a,(b,(c,d)))[&W 0.1][&color=wrong1];
[&W 0.1][&color=wrong1][&U];[&W 0.1][&color=wrong1];[&W 0.1][&color=wrong1];
[&color=red][&W 0.25][&R](a,(b,(c,d)))[&W 0.1][&color=wrong1];
[&W 0.1][&color=wrong1][&U];[&W 0.1][&color=wrong1];[&W 0.1][&color=wrong1];
(a,(b,(c,d)));;;
"""
trees = dendropy.TreeList.get_from_string(tree_str,
"newick",
extract_comment_metadata=True,
store_tree_weights=True)
self.assertEqual(len(trees.taxon_namespace), 4)
tax_labels = [t.label for t in trees.taxon_namespace]
self.assertSequenceEqual(set(tax_labels), set(["a", "b", "c", "d"]))
self.assertEqual(len(trees), 3)
for tree_idx, tree in enumerate(trees):
if tree_idx < 2:
self.assertIs(tree.is_rooted, True)
self.assertEqual(tree.weight, 0.25)
self.assertEqual(tree.annotations.get_value("color", None), "red")
else:
self.assertIs(tree.is_rooted, None)
self.assertEqual(tree.weight, 1.0)
self.assertFalse(tree.has_annotations)
class NewickTreeListReaderMultipleRedundantSemiColons(
curated_test_tree.CuratedTestTree,
dendropytest.ExtendedTestCase):
def test_multiple_redundant_semicolons(self):
tree_str = self.get_newick_string()
s = ";;;;;{tree_str};;; ;\n; \n ; ;;{tree_str};;; [(a,(b,c)]; ; ;;".format(tree_str=tree_str)
trees = dendropy.TreeList.get_from_string(s,
"newick",
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=False,
suppress_edge_lengths=False)
self.assertEqual(len(trees), 2)
for t in trees:
self.verify_curated_tree(t,
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=False,
suppress_edge_lengths=False)
class NewickTreeListReaderTaxonNamespaceTest(dendropytest.ExtendedTestCase):
def test_shared_taxon_namespace(self):
tree_filenames = [
("pythonidae.reference-trees.newick", 33), # ntax = 33
("pythonidae.reference-trees.newick", 33), # ntax = 33
("bird_orders.newick", 56), # ntax = 23
("pythonidae.reference-trees.taxon-numbers-only.newick", 89), # ntax = 33
("pythonidae.reference-trees.newick", 89), # ntax = 33
("bird_orders.newick", 89), # ntax = 23
]
common_taxon_namespace = dendropy.TaxonNamespace()
prev_expected_ntax = 0
for tree_filename, expected_ntax in tree_filenames:
self.assertEqual(len(common_taxon_namespace), prev_expected_ntax)
tree_filepath = pathmap.tree_source_path(tree_filename)
for reps in range(3):
tree_list = dendropy.TreeList.get_from_path(
pathmap.tree_source_path(tree_filename),
"newick",
taxon_namespace=common_taxon_namespace)
self.assertEqual(len(common_taxon_namespace), expected_ntax)
prev_expected_ntax = expected_ntax
if __name__ == "__main__":
unittest.main()
|
