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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 NEXUS 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_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 NexusStandardTreeParsingTestCase(
base_standard_trees_parsing_test_cases.StandardTreesParsingTestCase,
standard_file_test_trees.NexusTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NexusTestTreesChecker.create_class_fixtures(cls)
## NOTE: many tests are in standard_file_test_trees.StandardTreeParsingTestCase !! ##
def test_collection_comments_and_annotations(self):
for tree_file_title in (
"dendropy-test-trees-multifurcating-rooted-annotated",
"dendropy-test-trees-n33-unrooted-annotated-x10a",
):
tree_reference = dict(standard_file_test_trees._TREE_REFERENCES[tree_file_title])
expected_non_metadata_comments = tree_reference["tree_list_comments"]
expected_metadata = tree_reference["tree_list_metadata"]
tree_filepath = self.schema_tree_filepaths[tree_file_title]
tree_list = dendropy.TreeList.get_from_path(
tree_filepath,
"nexus")
expected_comments = expected_non_metadata_comments
self.compare_annotations_to_json_metadata_dict(
tree_list,
expected_metadata)
if self.__class__.is_check_comments:
self.assertEqual(len(tree_list.comments), len(expected_comments))
self.assertEqual(set(tree_list.comments), set(expected_comments))
self.verify_standard_trees(
tree_list=tree_list,
tree_file_title=tree_file_title,
tree_offset=0)
class NexusMultiTreeListTestCase(dendropytest.ExtendedTestCase):
def test_multiple_trees1(self):
src_filename = "multitreeblocks.nex"
src_path = pathmap.tree_source_path(src_filename)
trees = dendropy.TreeList.get_from_path(src_path, "nexus")
self.assertEqual(len(trees), 9)
def test_multiple_trees2(self):
src_filename = "multitreeblocks2.nex"
src_path = pathmap.tree_source_path(src_filename)
trees = dendropy.TreeList.get_from_path(src_path, "nexus")
self.assertEqual(len(trees), 4)
labels = ["x2.1","x2.2","x2.3","x2.4"]
# self.assertEqual(len(trees.taxon_namespace), len(labels))
self.assertEqual([t.label for t in trees.taxon_namespace], labels)
for tree in trees:
self.assertIs(tree.taxon_namespace, trees.taxon_namespace)
seen_taxa = 0
for nd in tree:
if nd.taxon is not None:
seen_taxa += 1
self.assertIn(nd.taxon, tree.taxon_namespace)
self.assertEqual(seen_taxa, len(tree.taxon_namespace))
class NexusStandardTreesWithTranslateBlockButNoTaxaBlockTestCase(
curated_test_tree.CuratedTestTree,
dendropytest.ExtendedTestCase):
def test_with_translate_but_no_taxa_block(self):
src_filename = "curated-with-translate-block-and-no-taxa-block-and-untranslated-internal-taxa.nex"
src_path = pathmap.tree_source_path(src_filename)
tree_list = dendropy.TreeList.get_from_path(src_path, "nexus")
tree_labels = ("1", "2", "3")
self.assertEqual(len(tree_list), len(tree_labels))
for tree_idx, (tree, label) in enumerate(zip(tree_list, tree_labels)):
self.assertEqual(tree.label, label)
self.verify_curated_tree(tree=tree)
if __name__ == "__main__":
unittest.main()
|
