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view 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
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import unittest
import os
from commons.core.utils.FileUtils import FileUtils
from commons.tools.tests.MockFastaForReplaceGreaterThanSymbolInFastaHeader import MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan,\
    MockFastaForReplaceGreaterThanSymbolInFastaHeader
from commons.tools.replaceGreaterThanSymbolInFastaHeaderProgramLauncher import replaceGreaterThanSymbolInFastaHeaderProgramLauncher

class Test_F_ReplaceGreaterThanSymbolInHeader(unittest.TestCase):


    def test_run(self):
        inputFileName = "dummy_fasta.fsa"
        mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader()
        mockInput.write(inputFileName)
        
        expFileName = "exp_dummy_fasta.preprocessed.fsa"
        mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan()
        mockInput.write(expFileName)
        
        obsFileName = "dummy_fasta.preprocessed.fasta"
        rgtspl = replaceGreaterThanSymbolInFastaHeaderProgramLauncher()
        rgtspl.setInputFile(inputFileName)
        rgtspl.run()
        
        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
        os.remove(inputFileName)
        os.remove(expFileName)
        os.remove(obsFileName)

    def test_run_as_script(self):
        inputFileName = "dummy_fasta.fsa"
        mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader()
        mockInput.write(inputFileName)
        
        expFileName = "exp_dummy_fasta.preprocessed.fsa"
        mockInput = MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan()
        mockInput.write(expFileName)
        
        obsFileName = "dummy_fasta.preprocessed.fasta"

        cmd2Launch = "replaceGreaterThanSymbolInFastaHeaderProgramLauncher.py -i " + inputFileName
        os.system(cmd2Launch)
        
        self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
        os.remove(inputFileName)       
        os.remove(expFileName)
        os.remove(obsFileName)    


if __name__ == "__main__":
    unittest.main()