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

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import unittest
from commons.launcher.MapProgramLauncher import MapProgramLauncher

class Test_MapProgramLauncher( unittest.TestCase ):
    
    def setUp( self ):
        self._i = MapProgramLauncher()
        
    def tearDown( self ):
        self._i = None
        
    def test_getSpecificHelpAsString( self ):
        exp = ""
        exp += "\nspecific options:"
        exp += "\n     -s: size above which a gap is not penalized anymore (default='%i')" % ( self._i.getGapSize() )
        exp += "\n     -m: penalty for a mismatch (default='%i', match=10)" % ( self._i.getMismatchPenalty() )
        exp += "\n     -O: penalty for a gap opening (default='%i')" % (  self._i.getGapOpenPenalty())
        exp += "\n     -e: penalty for a gap extension (default='%i')" % ( self._i.getGapExtendPenalty() )
        exp += "\n     -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
        obs = self._i.getSpecificHelpAsString()
        self.assertEqual( exp, obs )
        
    def test_setASpecificAttributeFromCmdLine( self ):
        self._i.setASpecificAttributeFromCmdLine( "-s", "40" )
        self.assertEqual( 40, self._i.getGapSize() )
        
        self._i.setASpecificAttributeFromCmdLine( "-m", "-7" )
        self.assertEqual( -7, self._i.getMismatchPenalty() )
        
        self._i.setASpecificAttributeFromCmdLine( "-O", "15" )
        self.assertEqual( 15, self._i.getGapOpenPenalty() )
        
        self._i.setASpecificAttributeFromCmdLine( "-e", "5" )
        self.assertEqual( 5, self._i.getGapExtendPenalty() )
        
        self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" )
        self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() )
        
    def test_setWrapperCommandLine( self ):
        inFile = "dummyInFile.fa"
        self._i.setInputFile( inFile )
        exp = "MapProgramLauncher.py"
        exp += " -i %s" % ( inFile )
        exp += " -s 50"
        exp += " -m -8"
        exp += " -O 16"
        exp += " -e 4"
        exp += " -o %s.fa_aln" % ( inFile )
        exp += " -v 0"
        self._i.setWrapperCommandLine()
        obs = self._i.getWrapperCommandLine()
        self.assertEqual( exp, obs )
        
    def test_setProgramCommandLine( self ):
        inFile = "dummyInFile.fa"
        self._i.setInputFile( inFile )
        exp = self._i.getProgramName()
        exp += " %s.shortH" % ( inFile )
        exp += " 50"
        exp += " -8"
        exp += " 16"
        exp += " 4"
        exp += " > %s.shortH.fa_aln" % ( inFile )
        self._i.setProgramCommandLine()
        obs = self._i.getProgramCommandLine()
        self.assertEqual( exp, obs )
        
    def test_setListFilesToKeep( self ):
        inFile = "dummyInFile.fa"
        self._i.setInputFile( inFile )
        self._i.setListFilesToKeep()
        lExp = [ "dummyInFile.fa.fa_aln" ]
        lObs = self._i.getListFilesToKeep()
        lExp.sort()
        lObs.sort()
        self.assertEqual( lExp, lObs )
        
        self._i._lFilesToKeep = []
        
        outFile = "dummyOutFile.fa_aln"
        self._i.setOutputFile( outFile )
        self._i.setListFilesToKeep()
        lExp = [ outFile ]
        lObs = self._i.getListFilesToKeep()
        lExp.sort()
        lObs.sort()
        self.assertEqual( lExp, lObs )
        
    def test_getListFilesToRemove( self ):
        inFile = "dummyInFile.fa"
        self._i.setInputFile( inFile )
        self._i.setListFilesToRemove()
        lExp = [ "dummyInFile.fa.shortH", \
                 "dummyInFile.fa.shortH.fa_aln", \
                 "dummyInFile.fa.shortHlink" ]
        lObs = self._i.getListFilesToRemove()
        lExp.sort()
        lObs.sort()
        self.assertEqual( lExp, lObs )
        
    def test_setSummary( self ):
        self._i.setInputFile( "dummyInFile.fa" )
        self._i.setGapSize( 104 )
        exp = "input file: %s" % ( "dummyInFile.fa" )
        exp += "\ngap size: %i" % ( self._i.getGapSize() )
        exp += "\nmismatch penalty: %i" % ( self._i.getMismatchPenalty() )
        exp += "\ngap openning penalty: %i" % ( self._i.getGapOpenPenalty() )
        exp += "\ngap extension penalty: %i" % ( self._i.getGapExtendPenalty() )
        exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" )
        self._i.setSummary()
        obs = self._i.getSummary()
        self.assertEqual( exp, obs )

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