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1 import unittest
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2 from commons.launcher.NWalignProgramLauncher import NWalignProgramLauncher
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3
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4
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5 class Test_NWalignProgramLauncher( unittest.TestCase ):
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6
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7 def setUp( self ):
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8 self._i = NWalignProgramLauncher()
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9
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10
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11 def tearDown( self ):
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12 self._i = None
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13
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14
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15 def test_getSpecificHelpAsString( self ):
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16 exp = ""
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17 exp += "\nspecific options:"
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18 exp += "\n -s: name of the subject file (format='fasta')"
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19 exp += "\n -p: parameters for 'NWalign'"
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20 exp += "\n -o: name of the output file (format='align', default=inFile+'.align')"
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21 obs = self._i.getSpecificHelpAsString()
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22 self.assertEqual( exp, obs )
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23
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24
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25 def test_setASpecificAttributeFromCmdLine( self ):
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26 self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
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27 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
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28
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29 self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
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30 self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
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31
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32
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33 def test_setWrapperCommandLine( self ):
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34 self._i.setInputFile( "dummyInFile.fa" )
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35 self._i.setSubjectFile( "dummySubjectFile.fa" )
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36 exp = "NWalignProgramLauncher.py"
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37 exp += " -i %s" % ( "dummyInFile.fa" )
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38 exp += " -s %s" % ( "dummySubjectFile.fa" )
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39 exp += " -o %s.align" % ( "dummyInFile.fa" )
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40 exp += " -v 0"
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41 self._i.setWrapperCommandLine()
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42 obs = self._i.getWrapperCommandLine()
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43 self.assertEqual( exp, obs )
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44
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45
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46 def test_setProgramCommandLine( self ):
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47 self._i.setInputFile( "dummyInFile.fa" )
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48 self._i.setSubjectFile( "dummySubjectFile.fa" )
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49 self._i.setProgramParameters( "-m 2" )
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50 exp = "NWalign -m 2 -o dummyInFile.fa.afa -v 0 dummySubjectFile.fa dummyInFile.fa"
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51 self._i.setProgramCommandLine()
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52 obs = self._i.getProgramCommandLine()
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53 self.assertEqual( exp, obs )
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54
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55
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56 def test_setListFilesToKeep( self ):
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57 self._i.setInputFile( "dummyInFile.fa" )
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58 lExp = [ "dummyInFile.fa.afa" ]
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59 self._i.setListFilesToKeep()
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60 lObs = self._i.getListFilesToKeep()
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61 lExp.sort()
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62 lObs.sort()
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63 self.assertEqual( lExp, lObs )
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64
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65
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66 def test_setSummary( self ):
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67 self._i.setInputFile( "dummyInFile.fa" )
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68 self._i.setSubjectFile( "dummySubjectFile.fa" )
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69 exp = "input file: %s" % ( self._i.getInputFile() )
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70 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
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71 exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
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72 exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
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73 self._i.setSummary()
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74 obs = self._i.getSummary()
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75 self.assertEqual( exp, obs )
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76
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77 if __name__ == "__main__":
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78 unittest.main() |