Mercurial > repos > yufei-luo > s_mart
comparison commons/tools/tests/Test_F_ReplaceGreaterThanSymbolInFastaHeader.py @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 import unittest | |
| 2 import os | |
| 3 from commons.core.utils.FileUtils import FileUtils | |
| 4 from commons.tools.tests.MockFastaForReplaceGreaterThanSymbolInFastaHeader import MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan,\ | |
| 5 MockFastaForReplaceGreaterThanSymbolInFastaHeader | |
| 6 from commons.tools.replaceGreaterThanSymbolInFastaHeaderProgramLauncher import replaceGreaterThanSymbolInFastaHeaderProgramLauncher | |
| 7 | |
| 8 class Test_F_ReplaceGreaterThanSymbolInHeader(unittest.TestCase): | |
| 9 | |
| 10 | |
| 11 def test_run(self): | |
| 12 inputFileName = "dummy_fasta.fsa" | |
| 13 mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader() | |
| 14 mockInput.write(inputFileName) | |
| 15 | |
| 16 expFileName = "exp_dummy_fasta.preprocessed.fsa" | |
| 17 mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan() | |
| 18 mockInput.write(expFileName) | |
| 19 | |
| 20 obsFileName = "dummy_fasta.preprocessed.fasta" | |
| 21 rgtspl = replaceGreaterThanSymbolInFastaHeaderProgramLauncher() | |
| 22 rgtspl.setInputFile(inputFileName) | |
| 23 rgtspl.run() | |
| 24 | |
| 25 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) | |
| 26 os.remove(inputFileName) | |
| 27 os.remove(expFileName) | |
| 28 os.remove(obsFileName) | |
| 29 | |
| 30 def test_run_as_script(self): | |
| 31 inputFileName = "dummy_fasta.fsa" | |
| 32 mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader() | |
| 33 mockInput.write(inputFileName) | |
| 34 | |
| 35 expFileName = "exp_dummy_fasta.preprocessed.fsa" | |
| 36 mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan() | |
| 37 mockInput.write(expFileName) | |
| 38 | |
| 39 obsFileName = "dummy_fasta.preprocessed.fasta" | |
| 40 | |
| 41 cmd2Launch = "replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py -i " + inputFileName | |
| 42 os.system(cmd2Launch) | |
| 43 | |
| 44 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) | |
| 45 os.remove(inputFileName) | |
| 46 os.remove(expFileName) | |
| 47 os.remove(obsFileName) | |
| 48 | |
| 49 | |
| 50 if __name__ == "__main__": | |
| 51 unittest.main() |