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
# test_sfffile.py
import hashlib
import os
import shutil
import tempfile
from cogent.util.unit_test import TestCase, main
from cogent.app.util import ApplicationError
from cogent.app.sfffile import Sfffile
__author__ = "Kyle Bittinger"
__copyright__ = "Copyright 2007-2010, The Cogent Project"
__credits__ = ["Kyle Bittinger"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
__status__ = "Prototype"
class SfffileTests(TestCase):
"""Test the Sfffile application controller.
"""
def setUp(self):
test_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.sff_fp = os.path.join(test_dir, 'data', 'test.sff')
def test_exit_status(self):
"""Sfffile should raise ApplicationError if exit status is nonzero."""
a = Sfffile()
self.assertRaises(ApplicationError, a, 'an_sff_file_that_does_not_exist.sff')
def test_call(self):
"""Simple sfffile call should produce expected output."""
a = Sfffile()
app_results = a(self.sff_fp)
# compare md5 digests
expected = hashlib.md5(open(self.sff_fp, 'rb').read()).hexdigest()
observed = hashlib.md5(app_results['sff'].read()).hexdigest()
self.assertEqual(observed, expected)
app_results.cleanUp()
def test_call_with_output_path(self):
"""Sfffile should store output to specified filepath."""
_, output_fp = tempfile.mkstemp()
a = Sfffile()
a.Parameters['-o'].on(output_fp)
app_results = a(self.sff_fp)
expected = hashlib.md5(open(self.sff_fp, 'rb').read()).hexdigest()
observed = hashlib.md5(open(output_fp, 'rb').read()).hexdigest()
self.assertEqual(observed, expected)
# Double check that app_results are still valid
observed = hashlib.md5(app_results['sff'].read()).hexdigest()
self.assertEqual(observed, expected)
app_results.cleanUp()
def test_call_with_included_accession_numbers(self):
"""Sfffile should include specified accession numbers in output."""
accno_file = tempfile.NamedTemporaryFile()
accno_file.write('FA6P1OK01CGMHQ\n')
accno_file.seek(0)
a = Sfffile()
a.Parameters['-i'].on(accno_file.name)
app_results = a(self.sff_fp)
expected = hashlib.md5(open(self.sff_fp, 'rb').read()).hexdigest()
observed = hashlib.md5(app_results['sff'].read()).hexdigest()
self.assertEqual(observed, expected)
app_results.cleanUp()
def test_call_with_excluded_accession_numbers(self):
"""Sfffile should exclude specified accession numbers in output."""
accno_file = tempfile.NamedTemporaryFile()
accno_file.write('FA6P1OK01CGMHQ\n')
accno_file.seek(0)
a = Sfffile()
a.Parameters['-e'].on(accno_file.name)
app_results = a(self.sff_fp)
expected = hashlib.md5(open(self.sff_fp, 'rb').read()).hexdigest()
observed = hashlib.md5(app_results['sff'].read()).hexdigest()
self.assertNotEqual(observed, expected)
app_results.cleanUp()
if __name__ == '__main__':
main()
|
