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
|
#!/usr/bin/env python
from os import getcwd, remove, rmdir, mkdir, path
import tempfile, shutil
from cogent.core.moltype import RNA
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.mafft import Mafft, align_unaligned_seqs, \
add_seqs_to_alignment, align_two_alignments
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
class GeneralSetUp(TestCase):
def setUp(self):
"""Mafft general setUp method for all tests"""
self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC',
'GCGGCUAUUAGAUCGUA']
self.labels1 = ['>1','>2','>3']
self.lines1 = flatten(zip(self.labels1,self.seqs1))
self.aligned1 = {'1': 'acugcuagcuaguagcguacgua',\
'2': 'gcuacguagcuac----------',\
'3': 'gcggcuauuagau------cgua',\
}
self.seqs2=['UAGGCUCUGAUAUAAUAGCUCUC','UAUCGCUUCGACGAUUCUCUGAUAGAGA',
'UGACUACGCAU']
self.labels2=['>a','>b','>c']
self.lines2 = flatten(zip(self.labels2,self.seqs2))
self.aligned2 = {'a': 'UAGGCUCUGAUAUAAUAGCUCUC---------',\
'b': 'UA----UCGCUUCGACGAUUCUCUGAUAGAGA',\
'c': 'UG------------ACUACGCAU---------',\
}
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test for mafft/'
try:
mkdir(self.temp_dir_spaces)
except OSError:
pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'),'w')
f.write('\n'.join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, 'seq2.txt'),'w')
g.write('\n'.join(self.lines2))
g.close()
except OSError:
pass
class MafftTests(GeneralSetUp):
"""Tests for the Mafft application controller"""
def test_base_command(self):
"""Mafft BaseCommand should return the correct BaseCommand"""
c = Mafft()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft']))
c.Parameters['--quiet'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft --quiet']))
c.Parameters['--globalpair'].on()
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ','mafft --globalpair --quiet']))
c.Parameters['--maxiterate'].on(1000)
self.assertEqual(c.BaseCommand,\
''.join(['cd "',getcwd(),'/"; ',"""mafft --maxiterate 1000 --globalpair --quiet"""]))
def test_changing_working_dir(self):
"""Mafft BaseCommand should change according to WorkingDir"""
c = Mafft(WorkingDir='/tmp/mafft_test')
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/mafft_test','/"; ','mafft']))
c = Mafft()
c.WorkingDir = '/tmp/mafft_test2'
self.assertEqual(c.BaseCommand,\
''.join(['cd "','/tmp/mafft_test2','/"; ','mafft']))
#removing the dirs is proof that they were created at the same time
#if the dirs are not there, an OSError will be raised
rmdir('/tmp/mafft_test')
rmdir('/tmp/mafft_test2')
def test_general_cleanUp(self):
"""Last test executed: cleans up all files initially created"""
# remove the tempdir and contents
shutil.rmtree(self.temp_dir)
shutil.rmtree(self.temp_dir_spaces)
def test_align_unaligned_seqs(self):
"""align_unaligned_seqs should work as expected"""
res = align_unaligned_seqs(self.seqs1, RNA)
self.assertEqual(res.toFasta(), align1)
res = align_unaligned_seqs(self.lines2, RNA)
self.assertEqual(res.toFasta(), align2)
def test_add_seqs_to_alignment(self):
"""add_seqs_to_alignment should work as expected."""
res = add_seqs_to_alignment(self.lines1,self.aligned2, RNA)
self.assertEqual(res.toFasta(), add_seqs_align)
def test_align_two_alignments(self):
"""align_two_alignments should work as expected."""
res = align_two_alignments(self.aligned1, self.aligned2, RNA)
self.assertEqual(res.toFasta(), align_two_align)
align1 = ">seq_0\nACUGCUAGCUAGUAGCGUACGUA\n>seq_1\nGCUACGUAGCUAC----------\n>seq_2\nGCGGCUAUUAGAU------CGUA"
align2 = ">a\nUAGGCUCUGAUAUAAUAGCUCUC---------\n>b\nUA----UCGCUUCGACGAUUCUCUGAUAGAGA\n>c\nUG------------ACUACGCAU---------"
add_seqs_align = """>1\nACUGC-UAGCUAGUAGCGUACGUA--------\n>2\nGCUACGUAGCUA-----------C--------\n>3\nGCGGCUAUUAGAUCGUA---------------\n>a\nUAGGCUCUGAUAUAAUAGCUCUC---------\n>b\nUA----UCGCUUCGACGAUUCUCUGAUAGAGA\n>c\nUG------------ACUACGCAU---------"""
align_two_align = """>1\nACUGCUAGCUAGUAGCGUACGUA---------\n>2\nGCUACGUAGCUAC-------------------\n>3\nGCGGCUAUUAGAU------CGUA---------\n>a\nUAGGCUCUGAUAUAAUAGCUCUC---------\n>b\nUA----UCGCUUCGACGAUUCUCUGAUAGAGA\n>c\nUG------------ACUACGCAU---------"""
if __name__ == '__main__':
main()
|
