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
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
|
#!/usr/bin/env python3
"""Execute the tests for the seqcons2 program.
The golden test outputs are generated by the script generate_outputs.sh.
You have to give the root paths to the source and the binaries as arguments to
the program. These are the paths to the directory that contains the 'projects'
directory.
Usage: run_tests.py SOURCE_ROOT_PATH BINARY_ROOT_PATH
"""
import logging
import os.path
import sys
# Automagically add util/py_lib to PYTHONPATH environment variable.
path = os.path.abspath(os.path.join(os.path.dirname(__file__), '..',
'..', '..', 'util', 'py_lib'))
sys.path.insert(0, path)
import seqan.app_tests as app_tests
def main(source_base, binary_base):
"""Main entry point of the script."""
print('Executing test for seqcons2')
print('===========================')
print()
ph = app_tests.TestPathHelper(
source_base, binary_base,
'apps/seqcons2/tests') # tests dir
# ============================================================
# Auto-detect the binary path.
# ============================================================
path_to_seqcons = app_tests.autolocateBinary(
binary_base, 'bin', 'seqcons2')
# ============================================================
# Built TestConf list.
# ============================================================
# Build list with TestConf objects, analoguely to how the output
# was generated in generate_outputs.sh.
conf_list = []
# We prepare a list of transforms to apply to the output files. This is
# used to strip the input/output paths from the programs' output to
# make it more canonical and host independent.
ph.outFile('-') # To ensure that the out path is set.
transforms = [
app_tests.ReplaceTransform(
os.path.join(ph.source_base_path,
'apps/seqcons2/tests') + os.sep,
'', right=True),
app_tests.ReplaceTransform(ph.temp_dir + os.sep, '', right=True),
app_tests.RegexpReplaceTransform(r'Overall time: .*s', r'Overall time: <removed>s', right=True, left=True),
app_tests.NormalizeScientificExponentsTransform(),
]
# ============================================================
# Test seqcons2
# ============================================================
# overlap_consensus and nop for FASTA input
for method in ['overlap_consensus', 'nop']:
conf = app_tests.TestConf(
program=path_to_seqcons,
args=['-m', method,
'-i', ph.inFile('alns1.sam'),
'-oc', ph.outFile('alns1.%s.fa' % method),
'-oa', ph.outFile('alns1.%s.sam' % method),
],
redir_stdout=ph.outFile('alns1.%s.sam.stdout' % method),
redir_stderr=ph.outFile('alns1.%s.sam.stderr' % method),
to_diff=[(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method)),
(ph.inFile('alns1.%s.sam' % method),
ph.outFile('alns1.%s.sam' % method)),
(ph.inFile('alns1.%s.sam.stderr' % method),
ph.outFile('alns1.%s.sam.stderr' % method),
transforms),
(ph.inFile('alns1.%s.sam.stdout' % method),
ph.outFile('alns1.%s.sam.stdout' % method),
transforms),
])
conf_list.append(conf)
# all consensus variants (except for align) for SAM input
for oa_ext in ['.sam', '.txt']:
for method in ['overlap_consensus', 'pos_consensus',
'contig_consensus', 'realign', 'nop']:
args = ['-m', method,
'-i', ph.inFile('alns1.sam'),
'-oa', ph.outFile('alns1.%s%s' % (method, oa_ext)),
]
to_diff = [(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method)),
(ph.inFile('alns1.%s%s' % (method, oa_ext)),
ph.outFile('alns1.%s%s' % (method, oa_ext))),
(ph.inFile('alns1.%s%s.stderr' % (method, oa_ext)),
ph.outFile('alns1.%s%s.stderr' % (method, oa_ext)),
transforms),
(ph.inFile('alns1.%s%s.stdout' % (method, oa_ext)),
ph.outFile('alns1.%s%s.stdout' % (method, oa_ext)),
transforms)
]
if oa_ext != '.txt':
args += ['-oc', ph.outFile('alns1.%s.fa' % method),]
to_diff += [(ph.inFile('alns1.%s.fa' % method),
ph.outFile('alns1.%s.fa' % method))]
conf = app_tests.TestConf(
program=path_to_seqcons,
args=args,
redir_stdout=ph.outFile('alns1.%s%s.stdout' % (method, oa_ext)),
redir_stderr=ph.outFile('alns1.%s%s.stderr' % (method, oa_ext)),
to_diff=to_diff)
conf_list.append(conf)
# align_consensus for longer sequences that are roughly globally similar
for oa_ext in ['.sam', '.txt']:
for method in ['align_consensus']:
args = ['-m', method,
'-i', ph.inFile('seqs2.fa'),
'-oa', ph.outFile('seqs2.%s%s' % (method, oa_ext)),
]
to_diff = [(ph.inFile('seqs2.%s.fa' % method),
ph.outFile('seqs2.%s.fa' % method)),
(ph.inFile('seqs2.%s%s' % (method, oa_ext)),
ph.outFile('seqs2.%s%s' % (method, oa_ext))),
(ph.inFile('seqs2.%s%s.stderr' % (method, oa_ext)),
ph.outFile('seqs2.%s%s.stderr' % (method, oa_ext)),
transforms),
(ph.inFile('seqs2.%s%s.stdout' % (method, oa_ext)),
ph.outFile('seqs2.%s%s.stdout' % (method, oa_ext)),
transforms)
]
if oa_ext != '.txt':
args += ['-oc', ph.outFile('seqs2.%s.fa' % method),]
to_diff += [(ph.inFile('seqs2.%s.fa' % method),
ph.outFile('seqs2.%s.fa' % method))]
conf = app_tests.TestConf(
program=path_to_seqcons,
args=args,
redir_stdout=ph.outFile('seqs2.%s%s.stdout' % (method, oa_ext)),
redir_stderr=ph.outFile('seqs2.%s%s.stderr' % (method, oa_ext)),
to_diff=to_diff)
conf_list.append(conf)
# Execute the tests.
failures = 0
for conf in conf_list:
res = app_tests.runTest(conf)
# Output to the user.
print(' '.join([os.path.basename(conf.program)] + conf.args), end=' ')
if res:
print('OK')
else:
failures += 1
print('FAILED')
# Cleanup.
ph.deleteTempDir()
print('==============================')
print(' total tests: %d' % len(conf_list))
print(' failed tests: %d' % failures)
print('successful tests: %d' % (len(conf_list) - failures))
print('==============================')
# Compute and return return code.
return failures != 0
if __name__ == '__main__':
sys.exit(app_tests.main(main))
|
