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

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import unittest
from commons.launcher.BlatProgramLauncher import BlatProgramLauncher


class Test_BlatProgramLauncher( unittest.TestCase ):
    
    def setUp( self ):
        self._i = BlatProgramLauncher()
        
        
    def tearDown( self ):
        self._i = None
        
        
    def test_getHelpAsString( self ):
        exp = ""
        exp += "usage: BlatProgramLauncher.py [options]" 
        exp += "\ngeneric options:"
        exp += "\n     -h: this help"
        exp += "\n     -i: name of the input file (format='fasta')"
        exp += "\n     -c: clean"
        exp += "\n     -v: verbosity level (default=0/1)"
        exp += "\nspecific options:"
        exp += "\n     -s: name of the subject file (database, format='fasta')"
        exp += "\n     -p: parameters for 'blat'"
        exp += "\n     -A: same sequences (all-by-all)"
        exp += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
        obs = self._i.getHelpAsString()
        self.assertEqual( exp, obs )
        
        
    def test_setAttributesFromCmdLine( self ):
        self._i.setAttributesFromCmdLine( "-s", "dummySubjectFile.fa" )
        self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
        
        self._i.setAttributesFromCmdLine( "-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 = "BlatProgramLauncher.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( "-minIdentity=90" )
        exp = "blat dummySubjectFile.fa dummyInFile.fa -minIdentity=90 -out=blast8 dummyInFile.fa.blast"
        self._i.setProgramCommandLine()
        obs = self._i.getProgramCommandLine()
        self.assertEqual( exp, obs )
        
        
    def test_setListFilesToKeep( self ):
        self._i.setInputFile( "dummyInFile.fa" )
        lExp = [ "dummyInFile.fa.align" ]
        self._i.setListFilesToKeep()
        lObs = self._i.getListFilesToKeep()
        lExp.sort()
        lObs.sort()
        self.assertEqual( lExp, lObs )
        
        
    def test_setListFilesToRemove( self ):
        self._i.setInputFile( "dummyInFile.fa" )
        lExp = [ "dummyInFile.fa.blast" ]
        self._i.setListFilesToRemove()
        lObs = self._i.getListFilesToRemove()
        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 )
        
        
test_suite = unittest.TestSuite()
test_suite.addTest( unittest.makeSuite( Test_BlatProgramLauncher ) )
if __name__ == "__main__":
    unittest.TextTestRunner(verbosity=2).run( test_suite )