Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_F_BlatProgramLauncher.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import os
2 import unittest
3 from commons.core.utils.FileUtils import FileUtils
4 from devTools.tests.MockFastaSupctg30 import MockFastaSupctg30
5 from devTools.tests.MockMiniProtBankSupctg30 import MockMiniProtBankSupctg30
6 from commons.launcher.tests.MockDataBankForBlat import MockDataBankForBlat
7 from commons.launcher.tests.MockESTBankForBlat import MockESTBankForBlat
8 from commons.launcher.tests.MockOutputForBlat import MockOutputForBlat
9 from commons.launcher.BlatProgramLauncher import BlatProgramLauncher
10
11 class Test_F_BlatProgramLauncher(unittest.TestCase):
12
13 def test_run_empty_result(self):
14 queryFileName = "smallProtBank_supctg30.fa"
15 mock = MockMiniProtBankSupctg30()
16 mock.write(queryFileName)
17 subjectFileName = "subjectBank.fa"
18 mock = MockFastaSupctg30()
19 mock.write(subjectFileName)
20
21 expOutputFileName = "expBlatOutput.blast.align"
22 self.writeEmptyExpOutputFile(expOutputFileName)
23
24 obsOutputFileName = "obsBlatOutput.blast.align"
25
26 bpl = BlatProgramLauncher()
27 bpl.setInputFile(queryFileName)
28 bpl.setSubjectFile(subjectFileName)
29 bpl.setOutputFile(obsOutputFileName)
30 bpl.setProgramParameters("")
31 bpl.run()
32
33 blastFileName = queryFileName + ".blast"
34
35 self.assertTrue(os.path.exists(obsOutputFileName))
36 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
37
38 os.remove(queryFileName)
39 os.remove(subjectFileName)
40 os.remove(blastFileName)
41 os.remove(expOutputFileName)
42 os.remove(obsOutputFileName)
43
44 def test_as_script_empty_result(self):
45 queryFileName = "smallProtBank_supctg30.fa"
46 mock = MockMiniProtBankSupctg30()
47 mock.write(queryFileName)
48 subjectFileName = "subjectBank.fa"
49 mock = MockFastaSupctg30()
50 mock.write(subjectFileName)
51
52 expOutputFileName = "expBlatOutput.blast.align"
53 self.writeEmptyExpOutputFile(expOutputFileName)
54
55 obsOutputFileName = "obsBlatOutput.blast.align"
56
57 cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName
58
59 os.system(cmd2Launch)
60
61 blastFileName = queryFileName + ".blast"
62
63 self.assertTrue(os.path.exists(obsOutputFileName))
64 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
65
66 os.remove(queryFileName)
67 os.remove(subjectFileName)
68 os.remove(blastFileName)
69 os.remove(expOutputFileName)
70 os.remove(obsOutputFileName)
71
72 def test_run(self):
73 queryFileName = "smallESTBank.fa"
74 mock = MockESTBankForBlat()
75 mock.write(queryFileName)
76 subjectFileName = "subjectBank.fa"
77 mock = MockDataBankForBlat()
78 mock.write(subjectFileName)
79
80 expOutputFileName = "expBlatOutput.blast.align"
81 mock = MockOutputForBlat()
82 mock.write(expOutputFileName)
83
84 obsOutputFileName = "obsBlatOutput.blast.align"
85
86 bpl = BlatProgramLauncher()
87 bpl.setInputFile(queryFileName)
88 bpl.setSubjectFile(subjectFileName)
89 bpl.setOutputFile(obsOutputFileName)
90 bpl.setProgramParameters("")
91 bpl.run()
92
93 blastFileName = queryFileName + ".blast"
94
95 self.assertTrue(os.path.exists(obsOutputFileName))
96 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
97
98 os.remove(queryFileName)
99 os.remove(subjectFileName)
100 os.remove(blastFileName)
101 os.remove(expOutputFileName)
102 os.remove(obsOutputFileName)
103
104 def test_as_script(self):
105 queryFileName = "smallESTBank.fa"
106 mock = MockESTBankForBlat()
107 mock.write(queryFileName)
108 subjectFileName = "subjectBank.fa"
109 mock = MockDataBankForBlat()
110 mock.write(subjectFileName)
111
112 expOutputFileName = "expBlatOutput.blast.align"
113 mock = MockOutputForBlat()
114 mock.write(expOutputFileName)
115
116 obsOutputFileName = "obsBlatOutput.blast.align"
117
118 cmd2Launch = "python ../BlatProgramLauncher.py -s " + subjectFileName + " -i " + queryFileName + " -p '' -o " + obsOutputFileName
119
120 os.system(cmd2Launch)
121
122 blastFileName = queryFileName + ".blast"
123
124 self.assertTrue(os.path.exists(obsOutputFileName))
125 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName))
126
127 os.remove(queryFileName)
128 os.remove(subjectFileName)
129 os.remove(blastFileName)
130 os.remove(expOutputFileName)
131 os.remove(obsOutputFileName)
132
133 def writeEmptyExpOutputFile(self, outputFileName):
134 f = open(outputFileName, "w")
135 f.write("")
136 f.close()
137
138 if __name__ == "__main__":
139 unittest.main()