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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
|
#!/usr/bin/env python
"""Tests for Stockholm sequence format writer.
"""
from cogent.util.unit_test import TestCase, main
from cogent.format.stockholm import stockholm_from_alignment
from cogent.core.alignment import Alignment
from cogent.core.sequence import Sequence
from cogent.core.info import Info
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Production"
class StockholmTests(TestCase):
"""Tests for Stockholm writer.
"""
def setUp(self):
"""Setup for Stockholm tests."""
self.unaligned_dict = {'1st':'AAA','2nd':'CCCC','3rd':'GGGG',
'4th':'UUUU'}
self.alignment_dict = {'1st':'AAAA','2nd':'CCCC','3rd':'GGGG',
'4th':'UUUU'}
#create alignment change order.
self.alignment_object = Alignment(self.alignment_dict)
self.alignment_order = ['2nd','4th','3rd','1st']
self.alignment_object.RowOrder=self.alignment_order
self.gc_annotation = {'SS_cons':'....'}
self.stockholm_with_label=\
"""# STOCKHOLM 1.0
1st AAAA
2nd CCCC
3rd GGGG
4th UUUU
//"""
self.stockholm_with_label_lw2=\
"""# STOCKHOLM 1.0
1st AA
2nd CC
3rd GG
4th UU
1st AA
2nd CC
3rd GG
4th UU
//"""
self.stockholm_with_label_struct=\
"""# STOCKHOLM 1.0
1st AAAA
2nd CCCC
3rd GGGG
4th UUUU
#=GC SS_cons ....
//"""
self.stockholm_with_label_struct_lw2=\
"""# STOCKHOLM 1.0
1st AA
2nd CC
3rd GG
4th UU
#=GC SS_cons ..
1st AA
2nd CC
3rd GG
4th UU
#=GC SS_cons ..
//"""
self.stockholm_with_label_reordered=\
"""# STOCKHOLM 1.0
2nd CCCC
4th UUUU
3rd GGGG
1st AAAA
//"""
self.stockholm_with_label_lw2_reordered=\
"""# STOCKHOLM 1.0
2nd CC
4th UU
3rd GG
1st AA
2nd CC
4th UU
3rd GG
1st AA
//"""
def test_stockholm_from_alignment_unaligned(self):
"""should raise error with unaligned seqs."""
self.assertRaises(ValueError,\
stockholm_from_alignment,self.unaligned_dict)
def test_stockholm_from_alignment(self):
"""should return correct stockholm string."""
self.assertEqual(stockholm_from_alignment({}),'')
self.assertEqual(stockholm_from_alignment(self.alignment_dict),\
self.stockholm_with_label)
self.assertEqual(stockholm_from_alignment(self.alignment_dict,
interleave_len=2),self.stockholm_with_label_lw2)
def test_stockholm_from_alignment_struct(self):
"""should return correct stockholm string."""
self.assertEqual(stockholm_from_alignment({},\
GC_annotation=self.gc_annotation),'')
self.assertEqual(stockholm_from_alignment(self.alignment_dict,\
GC_annotation=self.gc_annotation),\
self.stockholm_with_label_struct)
self.assertEqual(stockholm_from_alignment(self.alignment_dict,\
GC_annotation=self.gc_annotation,\
interleave_len=2),self.stockholm_with_label_struct_lw2)
def test_stockholm_from_alignment_reordered(self):
"""should return correct stockholm string."""
self.assertEqual(stockholm_from_alignment(self.alignment_object),\
self.stockholm_with_label_reordered)
self.assertEqual(stockholm_from_alignment(self.alignment_object,
interleave_len=2),self.stockholm_with_label_lw2_reordered)
if __name__ == "__main__":
main()
|
