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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 iteration 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 pathmap
if not (sys.version_info.major >= 3 and sys.version_info.minor >= 4):
from dendropy.utility.filesys import pre_py34_open as open
class NexusTreeYielderDefaultTestCase(
standard_file_test_trees.NexusTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NexusTestTreesChecker.create_class_fixtures(cls)
def test_basic(self):
tree_file_titles = [
# "dendropy-test-trees-multifurcating-rooted-annotated",
# "dendropy-test-trees-multifurcating-rooted",
# "dendropy-test-trees-multifurcating-unrooted",
# "dendropy-test-trees-n10-rooted-treeshapes",
"dendropy-test-trees-n12-x2",
"dendropy-test-trees-n33-unrooted-x10a",
"dendropy-test-trees-n33-unrooted-x10b",
"dendropy-test-trees-n33-unrooted-annotated-x10a",
"dendropy-test-trees-n33-unrooted-annotated-x10a",
]
expected_file_names = []
expected_tree_references = []
tree_files = []
for file_idx, tree_file_title in enumerate(tree_file_titles):
tree_filepath = self.schema_tree_filepaths[tree_file_title]
if False and idx % 2 == 0:
tree_files.append(open(tree_filepath, "r"))
else:
tree_files.append(tree_filepath)
num_trees = self.tree_references[tree_file_title]["num_trees"]
for tree_idx in range(num_trees):
expected_file_names.append(tree_filepath)
expected_tree_references.append(self.tree_references[tree_file_title][str(tree_idx)])
collected_trees = []
tns = dendropy.TaxonNamespace()
# for f in tree_files:
# dendropy.TreeList.get_from_path(f, "nexus")
tree_sources = dendropy.Tree.yield_from_files(
files=tree_files,
schema="nexus",
taxon_namespace=tns)
for tree_idx, tree in enumerate(tree_sources):
self.assertEqual(tree_sources.current_file_name, expected_file_names[tree_idx])
tree.current_file_name = tree_sources.current_file_name
collected_trees.append(tree)
self.assertEqual(len(collected_trees), len(expected_tree_references))
for tree, ref_tree in zip(collected_trees, expected_tree_references):
self.assertIs(tree.taxon_namespace, tns)
self.compare_to_reference_tree(tree, ref_tree)
## TODO:
# - test multiple trees blocks
# - mix of newick/nexus
if __name__ == "__main__":
unittest.main()
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