Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_MafftProgramLauncher.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.MafftProgramLauncher import MafftProgramLauncher
3
4 class Test_MafftProgramLauncher( unittest.TestCase ):
5
6
7 def setUp( self ):
8 self._i = MafftProgramLauncher()
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 -p: parameters for '%s' (default='--auto')" % ( "mafft" )
19 exp += "\n -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
20 obs = self._i.getSpecificHelpAsString()
21 self.assertEqual( exp, obs )
22
23
24 def test_setASpecificAttributeFromCmdLine( self ):
25 self._i.setASpecificAttributeFromCmdLine( "-p", "'--auto --maxiterate 500'" )
26 self.assertEqual( "'--auto --maxiterate 500'", self._i.getProgramParameters() )
27
28 self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" )
29 self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() )
30
31
32 def test_setWrapperCommandLine( self ):
33 inFile = "dummyInFile.fa"
34 self._i.setInputFile( inFile )
35 exp = "MafftProgramLauncher.py"
36 exp += " -i %s" % ( inFile )
37 exp += " -p '%s'" % ( "--auto" )
38 exp += " -o %s.fa_aln" % ( inFile )
39 exp += " -v 0"
40 self._i.setWrapperCommandLine()
41 obs = self._i.getWrapperCommandLine()
42 self.assertEqual( exp, obs )
43
44
45 def test_setProgramCommandLine( self ):
46 inFile = "dummyInFile.fa"
47 self._i.setInputFile( inFile )
48 exp = self._i.getProgramName()
49 exp += " %s" % ( "--auto" )
50 exp += " --quiet"
51 exp += " %s.shortH" % ( inFile )
52 exp += " > %s.shortH.fa_aln" % ( inFile )
53 exp += " 2> /dev/null"
54 self._i.setProgramCommandLine()
55 obs = self._i.getProgramCommandLine()
56 self.assertEqual( exp, obs )
57
58
59 def test_setListFilesToKeep( self ):
60 inFile = "dummyInFile.fa"
61 self._i.setInputFile( inFile )
62 self._i.setListFilesToKeep()
63 lExp = [ "dummyInFile.fa.fa_aln" ]
64 lObs = self._i.getListFilesToKeep()
65 lExp.sort()
66 lObs.sort()
67 self.assertEqual( lExp, lObs )
68
69 self._i._lFilesToKeep = []
70
71 outFile = "dummyOutFile.fa_aln"
72 self._i.setOutputFile( outFile )
73 self._i.setListFilesToKeep()
74 lExp = [ outFile ]
75 lObs = self._i.getListFilesToKeep()
76 lExp.sort()
77 lObs.sort()
78 self.assertEqual( lExp, lObs )
79
80
81 def test_setListFilesToRemove( self ):
82 inFile = "dummyInFile.fa"
83 self._i.setInputFile( inFile )
84 self._i.setListFilesToRemove()
85 lExp = [ "dummyInFile.fa.shortH", \
86 "dummyInFile.fa.shortH.fa_aln", \
87 "dummyInFile.fa.shortHlink" ]
88 lObs = self._i.getListFilesToRemove()
89 lExp.sort()
90 lObs.sort()
91 self.assertEqual( lExp, lObs )
92
93
94 def test_setSummary( self ):
95 self._i.setInputFile( "dummyInFile.fa" )
96 exp = "input file: %s" % ( "dummyInFile.fa" )
97 exp += "\nparameters: %s" % ( "--auto" )
98 exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" )
99 self._i.setSummary()
100 obs = self._i.getSummary()
101 self.assertEqual( exp, obs )
102
103
104 if __name__ == "__main__":
105 unittest.main()