view commons/launcher/tests/Test_NWalignProgramLauncher.py @ 18:94ab73e8a190

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import unittest
from commons.launcher.NWalignProgramLauncher import NWalignProgramLauncher


class Test_NWalignProgramLauncher( unittest.TestCase ):
    
    def setUp( self ):
        self._i = NWalignProgramLauncher()
        
        
    def tearDown( self ):
        self._i = None
        
        
    def test_getSpecificHelpAsString( self ):
        exp = ""
        exp += "\nspecific options:"
        exp += "\n     -s: name of the subject file (format='fasta')"
        exp += "\n     -p: parameters for 'NWalign'"
        exp += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
        obs = self._i.getSpecificHelpAsString()
        self.assertEqual( exp, obs )
        
        
    def test_setASpecificAttributeFromCmdLine( self ):
        self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
        
        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
        self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
        
        
    def test_setWrapperCommandLine( self ):
        self._i.setInputFile( "dummyInFile.fa" )
        self._i.setSubjectFile( "dummySubjectFile.fa" )
        exp = "NWalignProgramLauncher.py"
        exp += " -i %s" % ( "dummyInFile.fa" )
        exp += " -s %s" % ( "dummySubjectFile.fa" )
        exp += " -o %s.align" % ( "dummyInFile.fa" )
        exp += " -v 0"
        self._i.setWrapperCommandLine()
        obs = self._i.getWrapperCommandLine()
        self.assertEqual( exp, obs )
        
        
    def test_setProgramCommandLine( self ):
        self._i.setInputFile( "dummyInFile.fa" )
        self._i.setSubjectFile( "dummySubjectFile.fa" )
        self._i.setProgramParameters( "-m 2" )
        exp = "NWalign -m 2 -o dummyInFile.fa.afa -v 0 dummySubjectFile.fa dummyInFile.fa"
        self._i.setProgramCommandLine()
        obs = self._i.getProgramCommandLine()
        self.assertEqual( exp, obs )
        
        
    def test_setListFilesToKeep( self ):
        self._i.setInputFile( "dummyInFile.fa" )
        lExp = [ "dummyInFile.fa.afa" ]
        self._i.setListFilesToKeep()
        lObs = self._i.getListFilesToKeep()
        lExp.sort()
        lObs.sort()
        self.assertEqual( lExp, lObs )
        
        
    def test_setSummary( self ):
        self._i.setInputFile( "dummyInFile.fa" )
        self._i.setSubjectFile( "dummySubjectFile.fa" )
        exp = "input file: %s" % ( self._i.getInputFile() )
        exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
        exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
        exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
        self._i.setSummary()
        obs = self._i.getSummary()
        self.assertEqual( exp, obs )
        
if __name__ == "__main__":
        unittest.main()