Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_RepeatMaskerClusterLauncher.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 from commons.launcher.RepeatMaskerClusterLauncher import RepeatMaskerClusterLauncher
3
4
5 class Test_RepeatmaskerClusterLauncher( unittest.TestCase ):
6
7
8 def setUp( self ):
9 self._i = RepeatMaskerClusterLauncher()
10
11
12 def tearDown( self ):
13 self._i = None
14
15
16 def test_getSpecificHelpAsString( self ):
17 exp = ""
18 exp += "\nspecific options:"
19 exp += "\n -s: name of the subject file (repeats, format='fasta')"
20 exp += "\n -n: nb of processors to use in parallel (default=1)"
21 exp += "\n -g: calculate the GC content"
22 exp += "\n -b: skip bacterial insertion element check"
23 exp += "\n -l: mask low-complexity DNA or simple repeats"
24 obs = self._i.getSpecificHelpAsString()
25 self.assertEqual( exp, obs )
26
27
28 def test_setASpecificAttributeFromCmdLine( self ):
29 self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
30 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
31
32 self._i.setASpecificAttributeFromCmdLine( "-n", "2" )
33 self.assertEqual( 2, self._i.getNbProcessors() )
34
35 self._i.setASpecificAttributeFromCmdLine( "-g" )
36 self.assertTrue( self._i.getCalculateGCcontent() )
37
38 self._i.setASpecificAttributeFromCmdLine( "-b" )
39 self.assertTrue( self._i.getSkipBacterialIsCheck() )
40
41 self._i.setASpecificAttributeFromCmdLine( "-l" )
42 self.assertFalse( self._i.getMaskSsr() )
43
44 if __name__ == "__main__":
45 unittest.main()