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1 import unittest
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2 from commons.launcher.RepeatMaskerClusterLauncher import RepeatMaskerClusterLauncher
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3
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4
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5 class Test_RepeatmaskerClusterLauncher( unittest.TestCase ):
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6
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7
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8 def setUp( self ):
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9 self._i = RepeatMaskerClusterLauncher()
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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 (repeats, format='fasta')"
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20 exp += "\n -n: nb of processors to use in parallel (default=1)"
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21 exp += "\n -g: calculate the GC content"
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22 exp += "\n -b: skip bacterial insertion element check"
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23 exp += "\n -l: mask low-complexity DNA or simple repeats"
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24 obs = self._i.getSpecificHelpAsString()
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25 self.assertEqual( exp, obs )
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26
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27
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28 def test_setASpecificAttributeFromCmdLine( self ):
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29 self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
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30 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
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31
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32 self._i.setASpecificAttributeFromCmdLine( "-n", "2" )
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33 self.assertEqual( 2, self._i.getNbProcessors() )
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34
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35 self._i.setASpecificAttributeFromCmdLine( "-g" )
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36 self.assertTrue( self._i.getCalculateGCcontent() )
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37
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38 self._i.setASpecificAttributeFromCmdLine( "-b" )
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39 self.assertTrue( self._i.getSkipBacterialIsCheck() )
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40
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41 self._i.setASpecificAttributeFromCmdLine( "-l" )
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42 self.assertFalse( self._i.getMaskSsr() )
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43
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44 if __name__ == "__main__":
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45 unittest.main() |
