Mercurial > repos > yufei-luo > s_mart

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

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 import unittest
2 from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher
3
4
5 class Test_RepeatMaskerProgramLauncher( unittest.TestCase ):
6
7 def setUp( self ):
8 self._i = RepeatMaskerProgramLauncher()
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 (repeats, format='fasta')"
19 exp += "\n -n: nb of processors to use in parallel (default='%i')" % ( self._i.getNbProcessors() )
20 exp += "\n -g: calculate the GC content"
21 exp += "\n -b: skip bacterial insertion element check"
22 exp += "\n -l: does not mask low-complexity DNA or simple repeats"
23 exp += "\n -m: only masks low complex/simple repeats (no interspersed repeats)"
24 exp += "\n -o: name of the output file"
25 exp += "\n with -s: format='align', default=inFile+'.cat.align')"
26 exp += "\n with -m: format='path', default=inFile+'.cat.path')"
27 obs = self._i.getSpecificHelpAsString()
28 self.assertEqual( exp, obs )
29
30
31 def test_setASpecificAttributeFromCmdLine( self ):
32 self._i.setASpecificAttributeFromCmdLine( "-s", "dummySubjectFile.fa" )
33 self.assertEqual( "dummySubjectFile.fa", self._i.getSubjectFile() )
34
35 self._i.setASpecificAttributeFromCmdLine( "-n", "2" )
36 self.assertEqual( 2, self._i.getNbProcessors() )
37
38 self._i.setASpecificAttributeFromCmdLine( "-g" )
39 self.assertEqual( True, self._i.getCalculateGCcontent() )
40
41 self._i.setASpecificAttributeFromCmdLine( "-b" )
42 self.assertEqual( True, self._i.getSkipBacterialIsCheck() )
43
44 self._i.setASpecificAttributeFromCmdLine( "-l" )
45 self.assertEqual( False, self._i.getMaskSsr() )
46
47 self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.align" )
48 self.assertEqual( "dummyOutFile.align", self._i.getOutputFile() )
49
50
51 def test_setWrapperCommandLine( self ):
52 self._i.setInputFile( "dummyInFile.fa" )
53 self._i.setSubjectFile( "dummySubjectFile.fa" )
54 exp = "RepeatMaskerProgramLauncher.py"
55 exp += " -i %s" % ( "dummyInFile.fa" )
56 exp += " -s %s" % ( "dummySubjectFile.fa" )
57 exp += " -n 1"
58 self._i.setWrapperCommandLine()
59 obs = self._i.getWrapperCommandLine()
60 self.assertEqual( exp, obs )
61
62
63 def test_setProgramCommandLine( self ):
64 self._i.setInputFile( "dummyInFile.fa" )
65 self._i.setSubjectFile( "dummySubjectFile.fa" )
66 self._i.setCalculateGCcontent()
67 self._i.setSkipBacterialIsCheck()
68 exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow -lib dummySubjectFile.fa dummyInFile.fa"
69 self._i.setProgramCommandLine()
70 obs = self._i.getProgramCommandLine()
71 self.assertEqual( exp, obs )
72
73
74 def test_setProgramCommandLine_withoutSubjects_withMaskSsr( self ):
75 self._i.setInputFile( "dummyInFile.fa" )
76 self._i.setCalculateGCcontent()
77 self._i.setSkipBacterialIsCheck()
78 exp = "RepeatMasker -dir . -pa 1 -gccalc -no_is -nolow dummyInFile.fa"
79 self._i.setProgramCommandLine()
80 obs = self._i.getProgramCommandLine()
81 self.assertEqual( exp, obs )
82
83
84 def test_setListFilesToKeep_onlyInFile( self ):
85 self._i.setInputFile( "dummyInFile.fa" )
86 self._i.setOnlySsr()
87 lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.path" ]
88 self._i.setListFilesToKeep()
89 lObs = self._i.getListFilesToKeep()
90 lExp.sort()
91 lObs.sort()
92 self.assertEqual( lExp, lObs )
93
94
95 def test_setListFilesToKeep_withSubjectFile( self ):
96 self._i.setInputFile( "dummyInFile.fa" )
97 self._i.setSubjectFile( "dummySbjFile.fa" )
98 lExp = [ "dummyInFile.fa.cat", "dummyInFile.fa.cat.align" ]
99 self._i.setListFilesToKeep()
100 lObs = self._i.getListFilesToKeep()
101 lExp.sort()
102 lObs.sort()
103 self.assertEqual( lExp, lObs )
104
105
106 def test_setListFilesToKeep_inFileAndOutFile( self ):
107 self._i.setInputFile( "dummyInFile.fa" )
108 self._i.setOutputFile( "dummyOutFile.align" )
109 lExp = [ "dummyInFile.fa.cat", "dummyOutFile.align" ]
110 self._i.setListFilesToKeep()
111 lObs = self._i.getListFilesToKeep()
112 lExp.sort()
113 lObs.sort()
114 self.assertEqual( lExp, lObs )
115
116
117 def test_setListFilesToKeep_inFileAndOutFileAndSsr( self ):
118 self._i.setInputFile( "dummyInFile.fa" )
119 self._i.unsetMaskSsr()
120 self._i.setOutputFile( "dummyOutFile.path" )
121 lExp = [ "dummyInFile.fa.cat", "dummyOutFile.path" ]
122 self._i.setListFilesToKeep()
123 lObs = self._i.getListFilesToKeep()
124 lExp.sort()
125 lObs.sort()
126 self.assertEqual( lExp, lObs )
127
128
129 def test_setListFilesToRemove( self ):
130 self._i.setInputFile( "dummyInFile.fa" )
131 lExp = [ "dummyInFile.fa.out", \
132 "dummyInFile.fa.log", \
133 "dummyInFile.fa.stderr", \
134 "dummyInFile.fa.ori.out", \
135 "dummyInFile.fa.masked", \
136 "dummyInFile.fa.tbl", \
137 "dummyInFile.fa.ref" ]
138 self._i.setListFilesToRemove()
139 lObs = self._i.getListFilesToRemove()
140 lExp.sort()
141 lObs.sort()
142 self.assertEqual( lExp, lObs )
143
144
145 def test_setSummary( self ):
146 self._i.setInputFile( "dummyInFile.fa" )
147 self._i.setSubjectFile( "dummySubjectFile.fa" )
148 exp = "input file: %s" % ( self._i.getInputFile() )
149 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
150 exp += "\nnb processors: %i" % ( self._i.getNbProcessors() )
151 exp += "\nmask low-complexity DNA or simple repeats"
152 exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.path" )
153 self._i.setSummary()
154 obs = self._i.getSummary()
155 self.assertEqual( exp, obs )
156
157
158 def test_setSummary_noMaskSsr( self ):
159 self._i.setInputFile( "dummyInFile.fa" )
160 self._i.setSubjectFile( "dummySubjectFile.fa" )
161 self._i.unsetMaskSsr()
162 exp = "input file: %s" % ( self._i.getInputFile() )
163 exp += "\nsubject file: %s" % ( self._i.getSubjectFile() )
164 exp += "\nnb processors: %i" % ( self._i.getNbProcessors() )
165 exp += "\noutput file: %s" % ( "dummyInFile.fa.cat.align" )
166 self._i.setSummary()
167 obs = self._i.getSummary()
168 self.assertEqual( exp, obs )
169
170 if __name__ == "__main__":
171 unittest.main()