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