Mercurial > repos > yufei-luo > s_mart
view commons/launcher/tests/Test_RepeatMaskerProgramLauncher.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
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import unittest from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher class Test_RepeatMaskerProgramLauncher( unittest.TestCase ): def setUp( self ): self._i = RepeatMaskerProgramLauncher() def tearDown( self ): self._i = None def test_getSpecificHelpAsString( self ): exp = "" exp += "\nspecific options:" exp += "\n -s: name of the subject file (repeats, format='fasta')" exp += "\n -n: nb of processors to use in parallel (default='%i')" % ( self._i.getNbProcessors() ) exp += "\n -g: calculate the GC content" exp += "\n -b: skip bacterial insertion element check" exp += "\n -l: does not mask low-complexity DNA or simple repeats" exp += "\n -m: only masks low complex/simple repeats (no interspersed repeats)" exp += "\n -o: name of the output file" exp += "\n with -s: format='align', default=inFile+'.cat.align')" exp += "\n with -m: format='path', default=inFile+'.cat.path')" 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( "-n", "2" ) self.assertEqual( 2, self._i.getNbProcessors() ) self._i.setASpecificAttributeFromCmdLine( "-g" ) self.assertEqual( True, self._i.getCalculateGCcontent() ) self._i.setASpecificAttributeFromCmdLine( "-b" ) self.assertEqual( True, self._i.getSkipBacterialIsCheck() ) self._i.setASpecificAttributeFromCmdLine( "-l" ) self.assertEqual( False, self._i.getMaskSsr() ) 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 = "RepeatMaskerProgramLauncher.py" exp += " -i %s" % ( "dummyInFile.fa" ) exp += " -s %s" % ( "dummySubjectFile.fa" ) exp += " -n 1" 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.setCalculateGCcontent() self._i.setSkipBacterialIsCheck() exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow -lib dummySubjectFile.fa dummyInFile.fa" self._i.setProgramCommandLine() obs = self._i.getProgramCommandLine() self.assertEqual( exp, obs ) def test_setProgramCommandLine_withoutSubjects_withMaskSsr( self ): self._i.setInputFile( "dummyInFile.fa" ) self._i.setCalculateGCcontent() self._i.setSkipBacterialIsCheck() exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow dummyInFile.fa" self._i.setProgramCommandLine() obs = self._i.getProgramCommandLine() self.assertEqual( exp, obs ) def test_setListFilesToKeep_onlyInFile( self ): self._i.setInputFile( "dummyInFile.fa" ) self._i.setOnlySsr() lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.path" ] self._i.setListFilesToKeep() lObs = self._i.getListFilesToKeep() lExp.sort() lObs.sort() self.assertEqual( lExp, lObs ) def test_setListFilesToKeep_withSubjectFile( self ): self._i.setInputFile( "dummyInFile.fa" ) self._i.setSubjectFile( "dummySbjFile.fa" ) lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.align" ] self._i.setListFilesToKeep() lObs = self._i.getListFilesToKeep() lExp.sort() lObs.sort() self.assertEqual( lExp, lObs ) def test_setListFilesToKeep_inFileAndOutFile( self ): self._i.setInputFile( "dummyInFile.fa" ) self._i.setOutputFile( "dummyOutFile.align" ) lExp = [ "dummyInFile.fa.cat", "dummyOutFile.align" ] self._i.setListFilesToKeep() lObs = self._i.getListFilesToKeep() lExp.sort() lObs.sort() self.assertEqual( lExp, lObs ) def test_setListFilesToKeep_inFileAndOutFileAndSsr( self ): self._i.setInputFile( "dummyInFile.fa" ) self._i.unsetMaskSsr() self._i.setOutputFile( "dummyOutFile.path" ) lExp = [ "dummyInFile.fa.cat", "dummyOutFile.path" ] 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.out", \ "dummyInFile.fa.log", \ "dummyInFile.fa.stderr", \ "dummyInFile.fa.ori.out", \ "dummyInFile.fa.masked", \ "dummyInFile.fa.tbl", \ "dummyInFile.fa.ref" ] 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 += "\nnb processors: %i" % ( self._i.getNbProcessors() ) exp += "\nmask low-complexity DNA or simple repeats" exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.path" ) self._i.setSummary() obs = self._i.getSummary() self.assertEqual( exp, obs ) def test_setSummary_noMaskSsr( self ): self._i.setInputFile( "dummyInFile.fa" ) self._i.setSubjectFile( "dummySubjectFile.fa" ) self._i.unsetMaskSsr() exp = "input file: %s" % ( self._i.getInputFile() ) exp += "\nsubject file: %s" % ( self._i.getSubjectFile() ) exp += "\nnb processors: %i" % ( self._i.getNbProcessors() ) exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.align" ) self._i.setSummary() obs = self._i.getSummary() self.assertEqual( exp, obs ) if __name__ == "__main__": unittest.main()