Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
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30:5677346472b5 31:0ab839023fe4
1 import unittest
2 from commons.launcher.BlatProgramLauncher import BlatProgramLauncher
3
4
5 class Test_BlatProgramLauncher( unittest.TestCase ):
6
7 def setUp( self ):
8 self._i = BlatProgramLauncher()
9
10
11 def tearDown( self ):
12 self._i = None
13
14
15 def test_getHelpAsString( self ):
16 exp = ""
17 exp += "usage: BlatProgramLauncher.py [options]"
18 exp += "\ngeneric options:"
19 exp += "\n -h: this help"
20 exp += "\n -i: name of the input file (format='fasta')"
21 exp += "\n -c: clean"
22 exp += "\n -v: verbosity level (default=0/1)"
23 exp += "\nspecific options:"
24 exp += "\n -s: name of the subject file (database, format='fasta')"
25 exp += "\n -p: parameters for 'blat'"
26 exp += "\n -A: same sequences (all-by-all)"
27 exp += "\n -o: name of the output file (format='align', default=inFile+'.align')"
28 obs = self._i.getHelpAsString()
29 self.assertEqual( exp, obs )
30
31
32 def test_setAttributesFromCmdLine( self ):
33 self._i.setAttributesFromCmdLine( "-s", "dummySubjectFile.fa" )
34 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
35
36 self._i.setAttributesFromCmdLine( "-o", "dummyOutFile.align" )
37 self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
38
39
40 def test_setWrapperCommandLine( self ):
41 self._i.setInputFile( "dummyInFile.fa" )
42 self._i.setSubjectFile( "dummySubjectFile.fa" )
43 exp = "BlatProgramLauncher.py"
44 exp += " -i %s" % ( "dummyInFile.fa" )
45 exp += " -s %s" % ( "dummySubjectFile.fa" )
46 exp += " -o %s.align" % ( "dummyInFile.fa" )
47 exp += " -v 0"
48 self._i.setWrapperCommandLine()
49 obs = self._i.getWrapperCommandLine()
50 self.assertEqual( exp, obs )
51
52
53 def test_setProgramCommandLine( self ):
54 self._i.setInputFile( "dummyInFile.fa" )
55 self._i.setSubjectFile( "dummySubjectFile.fa" )
56 self._i.setProgramParameters( "-minIdentity=90" )
57 exp = "blat dummySubjectFile.fa dummyInFile.fa -minIdentity=90 -out=blast8 dummyInFile.fa.blast"
58 self._i.setProgramCommandLine()
59 obs = self._i.getProgramCommandLine()
60 self.assertEqual( exp, obs )
61
62
63 def test_setListFilesToKeep( self ):
64 self._i.setInputFile( "dummyInFile.fa" )
65 lExp = [ "dummyInFile.fa.align" ]
66 self._i.setListFilesToKeep()
67 lObs = self._i.getListFilesToKeep()
68 lExp.sort()
69 lObs.sort()
70 self.assertEqual( lExp, lObs )
71
72
73 def test_setListFilesToRemove( self ):
74 self._i.setInputFile( "dummyInFile.fa" )
75 lExp = [ "dummyInFile.fa.blast" ]
76 self._i.setListFilesToRemove()
77 lObs = self._i.getListFilesToRemove()
78 lExp.sort()
79 lObs.sort()
80 self.assertEqual( lExp, lObs )
81
82
83 def test_setSummary( self ):
84 self._i.setInputFile( "dummyInFile.fa" )
85 self._i.setSubjectFile( "dummySubjectFile.fa" )
86 exp = "input file: %s" % ( self._i.getInputFile() )
87 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
88 exp += "\nparameters: %s" % ( self._i.getProgramParameters() )
89 exp += "\noutput file: %s" % ( "dummyInFile.fa.align" )
90 self._i.setSummary()
91 obs = self._i.getSummary()
92 self.assertEqual( exp, obs )
93
94
95 test_suite = unittest.TestSuite()
96 test_suite.addTest( unittest.makeSuite( Test_BlatProgramLauncher ) )
97 if __name__ == "__main__":
98 unittest.TextTestRunner(verbosity=2).run( test_suite )