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
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
#! /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 dataset writing.
"""
import unittest
import dendropy
from dendropy.test.support import pathmap
from dendropy.test.support import dendropytest
from dendropy.test.support import compare_and_validate
from dendropy.test.support import standard_file_test_datasets
class DataSetNexusWriterMixedTestCase(
standard_file_test_datasets.StandardSingleTaxonNamespaceDataSet,
compare_and_validate.ValidateWriteable,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
standard_file_test_datasets.StandardSingleTaxonNamespaceDataSet.build(cls)
cls.check_taxon_annotations = False
cls.check_matrix_annotations = False
cls.check_sequence_annotations = False
cls.check_column_annotations = False
cls.check_cell_annotations = False
def get_source_dataset(self, **kwargs):
src_ds = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path("standard-test-mixed.1.basic.nexus"),
"nexus",
**kwargs
)
return src_ds
def test_basic(self):
# `suppress_internal_node_taxa=False` so internal labels get translated
d0 = self.get_source_dataset(suppress_internal_node_taxa=False)
s = self.write_out_validate_equal_and_return(
d0, "nexus", {})
ds = dendropy.DataSet.get_from_string(
s, "nexus",
suppress_internal_node_taxa=False, # so internal labels get translated
)
self.verify_dataset(ds)
class DataSetNexusWriterMesquiteMultipleTaxonNamespacesTest(
standard_file_test_datasets.MultipleTaxonNamespaceDataSet,
compare_and_validate.ValidateWriteable,
dendropytest.ExtendedTestCase):
def test_attached_taxon_namespace(self):
d0 = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('multitaxa_mesquite.nex'),
"nexus")
for tns in d0.taxon_namespaces:
d0.attach_taxon_namespace(tns)
s = self.write_out_validate_equal_and_return(
d0, "nexus", {})
ds = dendropy.DataSet.get_from_string(s, "nexus",)
self.verify_attached_taxon_namespace_written(ds, tns)
def test_default(self):
d0 = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('multitaxa_mesquite.nex'),
"nexus")
s = self.write_out_validate_equal_and_return(
d0, "nexus", {})
ds = dendropy.DataSet.get_from_string(
s, "nexus",
)
self.verify_unrestricted(ds)
if __name__ == "__main__":
unittest.main()
|
