Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 import unittest
2 from commons.launcher.YassProgramLauncher import YassProgramLauncher
3
4
5
6 class Test_YassProgramLauncher( unittest.TestCase ):
7
8 def setUp( self ):
9 self._i = YassProgramLauncher()
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 (format='fasta')"
20 exp += "\n -p: parameters for 'yass'"
21 exp += "\n -A: same sequences (all-by-all)"
22 exp += "\n -o: name of the output file (format='align', default=inFile+'.align')"
23 obs = self._i.getSpecificHelpAsString()
24 self.assertEqual( exp, obs )
25
26
27 def test_setASpecificAttributeFromCmdLine( self ):
28 self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
29 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
30
31 self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
32 self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
33
34
35 def test_setWrapperCommandLine( self ):
36 self._i.setInputFile( "dummyInFile.fa" )
37 self._i.setSubjectFile( "dummySubjectFile.fa" )
38 exp = "YassProgramLauncher.py"
39 exp += " -i %s" % ( "dummyInFile.fa" )
40 exp += " -s %s" % ( "dummySubjectFile.fa" )
41 exp += " -o %s.align" % ( "dummyInFile.fa" )
42 exp += " -v 0"
43 self._i.setWrapperCommandLine()
44 obs = self._i.getWrapperCommandLine()
45 self.assertEqual( exp, obs )
46
47
48 def test_setProgramCommandLine( self ):
49 self._i.setInputFile( "dummyInFile.fa" )
50 self._i.setSubjectFile( "dummySubjectFile.fa" )
51 exp = "yass -d 2 -o dummyInFile.fa.blast dummyInFile.fa dummySubjectFile.fa"
52 self._i.setProgramCommandLine()
53 obs = self._i.getProgramCommandLine()
54 self.assertEqual( exp, obs )
55
56
57 def test_setListFilesToKeep( self ):
58 self._i.setInputFile( "dummyInFile.fa" )
59 lExp = [ "dummyInFile.fa.align" ]
60 self._i.setListFilesToKeep()
61 lObs = self._i.getListFilesToKeep()
62 lExp.sort()
63 lObs.sort()
64 self.assertEqual( lExp, lObs )
65
66
67 def test_setSummary( self ):
68 self._i.setInputFile( "dummyInFile.fa" )
69 self._i.setSubjectFile( "dummySubjectFile.fa" )
70 exp = "input file: %s" % ( self._i.getInputFile() )
71 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
72 exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
73 exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
74 self._i.setSummary()
75 obs = self._i.getSummary()
76 self.assertEqual( exp, obs )
77
78 if __name__ == "__main__":
79 unittest.main()