Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_NWalignProgramLauncher.py @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
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30:5677346472b5 31:0ab839023fe4
1 import unittest
2 from commons.launcher.NWalignProgramLauncher import NWalignProgramLauncher
3
4
5 class Test_NWalignProgramLauncher( unittest.TestCase ):
6
7 def setUp( self ):
8 self._i = NWalignProgramLauncher()
9
10
11 def tearDown( self ):
12 self._i = None
13
14
15 def test_getSpecificHelpAsString( self ):
16 exp = ""
17 exp += "\nspecific options:"
18 exp += "\n -s: name of the subject file (format='fasta')"
19 exp += "\n -p: parameters for 'NWalign'"
20 exp += "\n -o: name of the output file (format='align', default=inFile+'.align')"
21 obs = self._i.getSpecificHelpAsString()
22 self.assertEqual( exp, obs )
23
24
25 def test_setASpecificAttributeFromCmdLine( self ):
26 self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
27 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
28
29 self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
30 self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
31
32
33 def test_setWrapperCommandLine( self ):
34 self._i.setInputFile( "dummyInFile.fa" )
35 self._i.setSubjectFile( "dummySubjectFile.fa" )
36 exp = "NWalignProgramLauncher.py"
37 exp += " -i %s" % ( "dummyInFile.fa" )
38 exp += " -s %s" % ( "dummySubjectFile.fa" )
39 exp += " -o %s.align" % ( "dummyInFile.fa" )
40 exp += " -v 0"
41 self._i.setWrapperCommandLine()
42 obs = self._i.getWrapperCommandLine()
43 self.assertEqual( exp, obs )
44
45
46 def test_setProgramCommandLine( self ):
47 self._i.setInputFile( "dummyInFile.fa" )
48 self._i.setSubjectFile( "dummySubjectFile.fa" )
49 self._i.setProgramParameters( "-m 2" )
50 exp = "NWalign -m 2 -o dummyInFile.fa.afa -v 0 dummySubjectFile.fa dummyInFile.fa"
51 self._i.setProgramCommandLine()
52 obs = self._i.getProgramCommandLine()
53 self.assertEqual( exp, obs )
54
55
56 def test_setListFilesToKeep( self ):
57 self._i.setInputFile( "dummyInFile.fa" )
58 lExp = [ "dummyInFile.fa.afa" ]
59 self._i.setListFilesToKeep()
60 lObs = self._i.getListFilesToKeep()
61 lExp.sort()
62 lObs.sort()
63 self.assertEqual( lExp, lObs )
64
65
66 def test_setSummary( self ):
67 self._i.setInputFile( "dummyInFile.fa" )
68 self._i.setSubjectFile( "dummySubjectFile.fa" )
69 exp = "input file: %s" % ( self._i.getInputFile() )
70 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
71 exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
72 exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
73 self._i.setSummary()
74 obs = self._i.getSummary()
75 self.assertEqual( exp, obs )
76
77 if __name__ == "__main__":
78 unittest.main()