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
|
#!/usr/bin/env python
"""Tests for Clustal sequence format writer.
"""
from cogent.util.unit_test import TestCase, main
from cogent.format.clustal import clustal_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 ClustalTests(TestCase):
"""Tests for Clustal writer.
"""
def setUp(self):
"""Setup for Clustal 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.clustal_with_label=\
"""CLUSTAL
1st AAAA
2nd CCCC
3rd GGGG
4th UUUU
"""
self.clustal_with_label_lw2=\
"""CLUSTAL
1st AA
2nd CC
3rd GG
4th UU
1st AA
2nd CC
3rd GG
4th UU
"""
self.clustal_with_label_reordered=\
"""CLUSTAL
2nd CCCC
4th UUUU
3rd GGGG
1st AAAA
"""
self.clustal_with_label_lw2_reordered=\
"""CLUSTAL
2nd CC
4th UU
3rd GG
1st AA
2nd CC
4th UU
3rd GG
1st AA
"""
def test_clustal_from_alignment_unaligned(self):
"""should raise error with unaligned seqs."""
self.assertRaises(ValueError,\
clustal_from_alignment,self.unaligned_dict)
def test_clustal_from_alignment(self):
"""should return correct clustal string."""
self.assertEqual(clustal_from_alignment({}),'')
self.assertEqual(clustal_from_alignment(self.alignment_dict),\
self.clustal_with_label)
self.assertEqual(clustal_from_alignment(self.alignment_dict,
interleave_len=2),self.clustal_with_label_lw2)
def test_clustal_from_alignment_reordered(self):
"""should return correct clustal string."""
self.assertEqual(clustal_from_alignment(self.alignment_object),\
self.clustal_with_label_reordered)
self.assertEqual(clustal_from_alignment(self.alignment_object,
interleave_len=2),self.clustal_with_label_lw2_reordered)
if __name__ == "__main__":
main()
|
