diff commons/launcher/tests/Test_MapProgramLauncher.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/tests/Test_MapProgramLauncher.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,115 @@
+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()
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