1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
|
#! /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 NEXUS tree list writing.
"""
import unittest
import dendropy
from dendropy.test.support import dendropytest
from dendropy.test.support import standard_file_test_trees
from dendropy.test.support import compare_and_validate
class NexusStandardTreeListWriterTestCase(
compare_and_validate.ValidateWriteable,
standard_file_test_trees.NexusTestTreesChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_trees.NexusTestTreesChecker.create_class_fixtures(cls)
def test_annotated_tree_list_writing(self):
tree_file_title = 'dendropy-test-trees-n33-unrooted-annotated-x10a'
tree_reference = standard_file_test_trees._TREE_REFERENCES[tree_file_title]
expected_non_metadata_comments = tree_reference["tree_list_comments"]
expected_metadata_comments = tree_reference["tree_list_metadata"]
expected_metadata = tree_reference["tree_list_metadata"]
tree_filepath = self.schema_tree_filepaths[tree_file_title]
tree_list1 = dendropy.TreeList.get_from_path(
tree_filepath,
"nexus",
extract_comment_metadata=True)
s = self.write_out_validate_equal_and_return(
tree_list1, "nexus", {})
tree_list2 = dendropy.TreeList.get_from_string(s,
"nexus",
extract_comment_metadata=True)
self.verify_standard_trees(
tree_list=tree_list2,
tree_file_title=tree_file_title,
tree_offset=0)
if __name__ == "__main__":
unittest.main()
|
