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
|
#!/usr/bin/env python
from os import remove
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.app.unafold import hybrid_ss_min
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.5.0"
__maintainer__ = "Shandy Wikman"
__email__ = "ens01svn@cs.umu.se"
__status__ = "Development"
class UnafoldTest(TestCase):
"""Tests for Unafold application controller"""
def setUp(self):
self.input = unafold_input
def test_stdout_input_as_lines(self):
"""Test Unafold stdout input as lines"""
u = hybrid_ss_min(InputHandler='_input_as_lines')
exp = '\n'.join(unafold_stdout)
res = u(self.input)
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
def test_stdout_input_as_string(self):
"""Test Unafold stdout input as string"""
u = hybrid_ss_min()
exp = '\n'.join(unafold_stdout)
f = open('/tmp/single.fasta','w')
f.write('\n'.join(self.input))
f.close()
res = u('/tmp/single.fasta')
obs = res['StdOut'].read()
self.assertEqual(obs,exp)
self.assertEqual(res['ExitStatus'],0)
res.cleanUp()
remove('/tmp/single.fasta')
def test_get_result_path(self):
"""Tests unafold result path"""
u = hybrid_ss_min(InputHandler='_input_as_lines')
res = u(self.input)
self.assertEqualItems(res.keys(),['StdOut','StdErr','ExitStatus',\
'ct','dG','run','plot_37','ext_37'])
self.assertEqual(res['ExitStatus'],0)
assert res['ct'] is not None
assert res['dG'] is not None
assert res['run'] is not None
assert res['plot_37'] is not None
assert res['ext_37'] is not None
res.cleanUp()
unafold_input = ['>seq1\n',
'GGCUAGAUAGCUCAGAUGGUAGAGCAGAGGAUUGAAGAUCCUUGUGUCGUCGGUUCGAUCCCGGCUCUGGC\n',
'\n']
unafold_stdout = ['Calculating for seq1, t = 37\n']
if __name__ == '__main__':
main()
|