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1 import unittest
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2 from commons.launcher.MapProgramLauncher import MapProgramLauncher
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3
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4 class Test_MapProgramLauncher( unittest.TestCase ):
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5
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6 def setUp( self ):
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7 self._i = MapProgramLauncher()
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8
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9 def tearDown( self ):
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10 self._i = None
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11
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12 def test_getSpecificHelpAsString( self ):
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13 exp = ""
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14 exp += "\nspecific options:"
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15 exp += "\n -s: size above which a gap is not penalized anymore (default='%i')" % ( self._i.getGapSize() )
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16 exp += "\n -m: penalty for a mismatch (default='%i', match=10)" % ( self._i.getMismatchPenalty() )
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17 exp += "\n -O: penalty for a gap opening (default='%i')" % ( self._i.getGapOpenPenalty())
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18 exp += "\n -e: penalty for a gap extension (default='%i')" % ( self._i.getGapExtendPenalty() )
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19 exp += "\n -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
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20 obs = self._i.getSpecificHelpAsString()
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21 self.assertEqual( exp, obs )
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22
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23 def test_setASpecificAttributeFromCmdLine( self ):
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24 self._i.setASpecificAttributeFromCmdLine( "-s", "40" )
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25 self.assertEqual( 40, self._i.getGapSize() )
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26
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27 self._i.setASpecificAttributeFromCmdLine( "-m", "-7" )
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28 self.assertEqual( -7, self._i.getMismatchPenalty() )
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29
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30 self._i.setASpecificAttributeFromCmdLine( "-O", "15" )
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31 self.assertEqual( 15, self._i.getGapOpenPenalty() )
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32
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33 self._i.setASpecificAttributeFromCmdLine( "-e", "5" )
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34 self.assertEqual( 5, self._i.getGapExtendPenalty() )
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35
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36 self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" )
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37 self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() )
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38
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39 def test_setWrapperCommandLine( self ):
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40 inFile = "dummyInFile.fa"
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41 self._i.setInputFile( inFile )
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42 exp = "MapProgramLauncher.py"
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43 exp += " -i %s" % ( inFile )
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44 exp += " -s 50"
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45 exp += " -m -8"
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46 exp += " -O 16"
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47 exp += " -e 4"
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48 exp += " -o %s.fa_aln" % ( inFile )
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49 exp += " -v 0"
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50 self._i.setWrapperCommandLine()
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51 obs = self._i.getWrapperCommandLine()
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52 self.assertEqual( exp, obs )
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53
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54 def test_setProgramCommandLine( self ):
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55 inFile = "dummyInFile.fa"
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56 self._i.setInputFile( inFile )
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57 exp = self._i.getProgramName()
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58 exp += " %s.shortH" % ( inFile )
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59 exp += " 50"
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60 exp += " -8"
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61 exp += " 16"
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62 exp += " 4"
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63 exp += " > %s.shortH.fa_aln" % ( inFile )
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64 self._i.setProgramCommandLine()
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65 obs = self._i.getProgramCommandLine()
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66 self.assertEqual( exp, obs )
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67
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68 def test_setListFilesToKeep( self ):
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69 inFile = "dummyInFile.fa"
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70 self._i.setInputFile( inFile )
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71 self._i.setListFilesToKeep()
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72 lExp = [ "dummyInFile.fa.fa_aln" ]
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73 lObs = self._i.getListFilesToKeep()
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74 lExp.sort()
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75 lObs.sort()
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76 self.assertEqual( lExp, lObs )
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77
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78 self._i._lFilesToKeep = []
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79
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80 outFile = "dummyOutFile.fa_aln"
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81 self._i.setOutputFile( outFile )
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82 self._i.setListFilesToKeep()
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83 lExp = [ outFile ]
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84 lObs = self._i.getListFilesToKeep()
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85 lExp.sort()
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86 lObs.sort()
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87 self.assertEqual( lExp, lObs )
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88
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89 def test_getListFilesToRemove( self ):
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90 inFile = "dummyInFile.fa"
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91 self._i.setInputFile( inFile )
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92 self._i.setListFilesToRemove()
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93 lExp = [ "dummyInFile.fa.shortH", \
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94 "dummyInFile.fa.shortH.fa_aln", \
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95 "dummyInFile.fa.shortHlink" ]
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96 lObs = self._i.getListFilesToRemove()
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97 lExp.sort()
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98 lObs.sort()
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99 self.assertEqual( lExp, lObs )
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100
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101 def test_setSummary( self ):
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102 self._i.setInputFile( "dummyInFile.fa" )
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103 self._i.setGapSize( 104 )
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104 exp = "input file: %s" % ( "dummyInFile.fa" )
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105 exp += "\ngap size: %i" % ( self._i.getGapSize() )
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106 exp += "\nmismatch penalty: %i" % ( self._i.getMismatchPenalty() )
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107 exp += "\ngap openning penalty: %i" % ( self._i.getGapOpenPenalty() )
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108 exp += "\ngap extension penalty: %i" % ( self._i.getGapExtendPenalty() )
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109 exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" )
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110 self._i.setSummary()
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111 obs = self._i.getSummary()
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112 self.assertEqual( exp, obs )
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113
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114 if __name__ == "__main__":
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115 unittest.main() |
