view commons/launcher/tests/Test_MafftProgramLauncher.py @ 31:0ab839023fe4

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import unittest
from commons.launcher.MafftProgramLauncher import MafftProgramLauncher

class Test_MafftProgramLauncher( unittest.TestCase ):
    
    
    def setUp( self ):
        self._i = MafftProgramLauncher()
        
        
    def tearDown( self ):
        self._i = None
        
        
    def test_getSpecificHelpAsString( self ):
        exp = ""
        exp += "\nspecific options:"
        exp += "\n     -p: parameters for '%s' (default='--auto')" % ( "mafft" )
        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( "-p", "'--auto --maxiterate 500'" )
        self.assertEqual( "'--auto --maxiterate 500'", self._i.getProgramParameters() )
        
        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 = "MafftProgramLauncher.py"
        exp += " -i %s" % ( inFile )
        exp += " -p '%s'" % ( "--auto" )
        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" % ( "--auto" )
        exp += " --quiet"
        exp += " %s.shortH" % ( inFile )
        exp += " > %s.shortH.fa_aln" % ( inFile )
        exp += " 2> /dev/null"
        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_setListFilesToRemove( 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" )
        exp = "input file: %s" % ( "dummyInFile.fa" )
        exp += "\nparameters: %s" % ( "--auto" )
        exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" )
        self._i.setSummary()
        obs = self._i.getSummary()
        self.assertEqual( exp, obs )
        
        
if __name__ == "__main__":
        unittest.main()