Mercurial > repos > yufei-luo > s_mart

annotate commons/tools/tests/Test_F_ReplaceGreaterThanSymbolInFastaHeader.py @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
1 import unittest
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
2 import os
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
3 from commons.core.utils.FileUtils import FileUtils
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
4 from commons.tools.tests.MockFastaForReplaceGreaterThanSymbolInFastaHeader import MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan,\
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
5 MockFastaForReplaceGreaterThanSymbolInFastaHeader
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
6 from commons.tools.replaceGreaterThanSymbolInFastaHeaderProgramLauncher import replaceGreaterThanSymbolInFastaHeaderProgramLauncher
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
7
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
8 class Test_F_ReplaceGreaterThanSymbolInHeader(unittest.TestCase):
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
9
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
10
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
11 def test_run(self):
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
12 inputFileName = "dummy_fasta.fsa"
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
13 mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader()
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
14 mockInput.write(inputFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
15
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
16 expFileName = "exp_dummy_fasta.preprocessed.fsa"
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
17 mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan()
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
18 mockInput.write(expFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
19
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
20 obsFileName = "dummy_fasta.preprocessed.fasta"
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
21 rgtspl = replaceGreaterThanSymbolInFastaHeaderProgramLauncher()
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
22 rgtspl.setInputFile(inputFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
23 rgtspl.run()
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
24
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
25 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
26 os.remove(inputFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
27 os.remove(expFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
28 os.remove(obsFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
29
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
30 def test_run_as_script(self):
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
31 inputFileName = "dummy_fasta.fsa"
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
32 mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader()
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
33 mockInput.write(inputFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
34
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
35 expFileName = "exp_dummy_fasta.preprocessed.fsa"
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
36 mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan()
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
37 mockInput.write(expFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
38
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
39 obsFileName = "dummy_fasta.preprocessed.fasta"
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
40
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
41 cmd2Launch = "replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py -i " + inputFileName
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
42 os.system(cmd2Launch)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
43
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
44 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
45 os.remove(inputFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
46 os.remove(expFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
47 os.remove(obsFileName)
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
48
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
49
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
50 if __name__ == "__main__":
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
51 unittest.main()