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1 import unittest
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2 from commons.launcher.BlatProgramLauncher import BlatProgramLauncher
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3
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4
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5 class Test_BlatProgramLauncher( unittest.TestCase ):
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6
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7 def setUp( self ):
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8 self._i = BlatProgramLauncher()
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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_getHelpAsString( self ):
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16 exp = ""
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17 exp += "usage: BlatProgramLauncher.py [options]"
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18 exp += "\ngeneric options:"
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19 exp += "\n -h: this help"
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20 exp += "\n -i: name of the input file (format='fasta')"
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21 exp += "\n -c: clean"
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22 exp += "\n -v: verbosity level (default=0/1)"
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23 exp += "\nspecific options:"
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24 exp += "\n -s: name of the subject file (database, format='fasta')"
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25 exp += "\n -p: parameters for 'blat'"
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26 exp += "\n -A: same sequences (all-by-all)"
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27 exp += "\n -o: name of the output file (format='align', default=inFile+'.align')"
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28 obs = self._i.getHelpAsString()
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29 self.assertEqual( exp, obs )
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30
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31
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32 def test_setAttributesFromCmdLine( self ):
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33 self._i.setAttributesFromCmdLine( "-s", "dummySubjectFile.fa" )
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34 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
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35
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36 self._i.setAttributesFromCmdLine( "-o", "dummyOutFile.align" )
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37 self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
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38
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39
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40 def test_setWrapperCommandLine( self ):
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41 self._i.setInputFile( "dummyInFile.fa" )
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42 self._i.setSubjectFile( "dummySubjectFile.fa" )
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43 exp = "BlatProgramLauncher.py"
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44 exp += " -i %s" % ( "dummyInFile.fa" )
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45 exp += " -s %s" % ( "dummySubjectFile.fa" )
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46 exp += " -o %s.align" % ( "dummyInFile.fa" )
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47 exp += " -v 0"
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48 self._i.setWrapperCommandLine()
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49 obs = self._i.getWrapperCommandLine()
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50 self.assertEqual( exp, obs )
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51
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52
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53 def test_setProgramCommandLine( self ):
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54 self._i.setInputFile( "dummyInFile.fa" )
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55 self._i.setSubjectFile( "dummySubjectFile.fa" )
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56 self._i.setProgramParameters( "-minIdentity=90" )
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57 exp = "blat dummySubjectFile.fa dummyInFile.fa -minIdentity=90 -out=blast8 dummyInFile.fa.blast"
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58 self._i.setProgramCommandLine()
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59 obs = self._i.getProgramCommandLine()
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60 self.assertEqual( exp, obs )
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61
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62
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63 def test_setListFilesToKeep( self ):
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64 self._i.setInputFile( "dummyInFile.fa" )
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65 lExp = [ "dummyInFile.fa.align" ]
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66 self._i.setListFilesToKeep()
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67 lObs = self._i.getListFilesToKeep()
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68 lExp.sort()
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69 lObs.sort()
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70 self.assertEqual( lExp, lObs )
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71
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72
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73 def test_setListFilesToRemove( self ):
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74 self._i.setInputFile( "dummyInFile.fa" )
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75 lExp = [ "dummyInFile.fa.blast" ]
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76 self._i.setListFilesToRemove()
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77 lObs = self._i.getListFilesToRemove()
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78 lExp.sort()
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79 lObs.sort()
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80 self.assertEqual( lExp, lObs )
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81
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82
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83 def test_setSummary( self ):
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84 self._i.setInputFile( "dummyInFile.fa" )
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85 self._i.setSubjectFile( "dummySubjectFile.fa" )
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86 exp = "input file: %s" % ( self._i.getInputFile() )
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87 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
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88 exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
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89 exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
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90 self._i.setSummary()
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91 obs = self._i.getSummary()
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92 self.assertEqual( exp, obs )
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93
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94
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95 test_suite = unittest.TestSuite()
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96 test_suite.addTest( unittest.makeSuite( Test_BlatProgramLauncher ) )
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97 if __name__ == "__main__":
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98 unittest.TextTestRunner(verbosity=2).run( test_suite )
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