Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/commons/core/parsing/test/Test_VarscanHit_WithTag.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 import unittest
2 from commons.core.checker.CheckerException import CheckerException
3 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
4
5 class Test_VarscanHit_WithTag(unittest.TestCase):
6
7 def test_setAttributesFromString(self):
8 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\tEspeceA\n"
9
10 expChrom = "chr1"
11 expPosition = "1804"
12 expRef = "T"
13 expVar = "C"
14 expReadsRef = "0"
15 expReadsVar = "1"
16 expVarFreq = "100%"
17 expStrandsRef = "0"
18 expStrandsVar = "1"
19 expQualRef = "0"
20 expQualVar = "53"
21 expPValue = "0.98"
22 expTag = "EspeceA"
23
24 varscanHit = VarscanHit_WithTag()
25 varscanHit.setAttributesFromString(line)
26
27 obsChrom = varscanHit.getChrom()
28 obsPosition = varscanHit.getPosition()
29 obsRef = varscanHit.getRef()
30 obsVar = varscanHit.getVar()
31 obsReadsRef = varscanHit.getReadsRef()
32 obsReadsVar = varscanHit.getReadsVar()
33 obsVarFreq = varscanHit.getVarFreq()
34 obsStrandsRef = varscanHit.getStrandsRef()
35 obsStrandsVar = varscanHit.getStrandsVar()
36 obsQualRef = varscanHit.getQualRef()
37 obsQualVar = varscanHit.getQualVar()
38 obsPValue = varscanHit.getPValue()
39 obsTag = varscanHit.getTag()
40
41 self.assertEquals(expChrom, obsChrom)
42 self.assertEquals(expPosition, obsPosition)
43 self.assertEquals(expRef, obsRef)
44 self.assertEquals(expVar, obsVar)
45 self.assertEquals(expReadsRef, obsReadsRef)
46 self.assertEquals(expReadsVar, obsReadsVar)
47 self.assertEquals(expVarFreq, obsVarFreq)
48 self.assertEquals(expStrandsRef, obsStrandsRef)
49 self.assertEquals(expStrandsVar, obsStrandsVar)
50 self.assertEquals(expQualRef, obsQualRef)
51 self.assertEquals(expQualVar, obsQualVar)
52 self.assertEquals(expPValue, obsPValue)
53 self.assertEquals(expTag, obsTag)
54
55 def test_setAttributesFromString_empty_chrom(self):
56 line = "\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\tEspeceA\n"
57 varscanHit = VarscanHit_WithTag()
58 try :
59 varscanHit.setAttributesFromString(line)
60 except CheckerException, e:
61 checkerExceptionInstance = e
62 expMessage = "The field Chrom is empty in varscan file in line "
63 obsMessage = checkerExceptionInstance.msg
64 self.assertEquals(expMessage, obsMessage)
65
66 def test_setAttributes(self):
67 lResults = ['chr1', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA']
68 lineNumber = 1
69
70 expChrom = "chr1"
71 expPosition = "1804"
72 expRef = "T"
73 expVar = "C"
74 expReadsRef = "0"
75 expReadsVar = "1"
76 expVarFreq = "100%"
77 expStrandsRef = "0"
78 expStrandsVar = "1"
79 expQualRef = "0"
80 expQualVar = "53"
81 expPValue = "0.98"
82 expTag = "EspeceA"
83
84 varscanHit = VarscanHit_WithTag()
85 varscanHit.setAttributes(lResults, lineNumber)
86
87 obsChrom = varscanHit.getChrom()
88 obsPosition = varscanHit.getPosition()
89 obsRef = varscanHit.getRef()
90 obsVar = varscanHit.getVar()
91 obsReadsRef = varscanHit.getReadsRef()
92 obsReadsVar = varscanHit.getReadsVar()
93 obsVarFreq = varscanHit.getVarFreq()
94 obsStrandsRef = varscanHit.getStrandsRef()
95 obsStrandsVar = varscanHit.getStrandsVar()
96 obsQualRef = varscanHit.getQualRef()
97 obsQualVar = varscanHit.getQualVar()
98 obsPValue = varscanHit.getPValue()
99 obsTag = varscanHit.getTag()
100
101 self.assertEquals(expChrom, obsChrom)
102 self.assertEquals(expPosition, obsPosition)
103 self.assertEquals(expRef, obsRef)
104 self.assertEquals(expVar, obsVar)
105 self.assertEquals(expReadsRef, obsReadsRef)
106 self.assertEquals(expReadsVar, obsReadsVar)
107 self.assertEquals(expVarFreq, obsVarFreq)
108 self.assertEquals(expStrandsRef, obsStrandsRef)
109 self.assertEquals(expStrandsVar, obsStrandsVar)
110 self.assertEquals(expQualRef, obsQualRef)
111 self.assertEquals(expQualVar, obsQualVar)
112 self.assertEquals(expPValue, obsPValue)
113 self.assertEquals(expTag, obsTag)
114
115 def test_setAttributes_empty_chrom(self):
116 lResults = ['', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA']
117 lineNumber = 1
118
119 varscanHit = VarscanHit_WithTag()
120 checkerExceptionInstance = None
121 try:
122 varscanHit.setAttributes(lResults, lineNumber)
123 except CheckerException, e:
124 checkerExceptionInstance = e
125
126 expMessage = "The field Chrom is empty in varscan file in line 1"
127 obsMessage = checkerExceptionInstance.msg
128
129 self.assertEquals(expMessage, obsMessage)
130
131 def test_setAttributes_empty_position(self):
132 lResults = ['chr1', '', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA']
133 lineNumber = 1
134
135 varscanHit = VarscanHit_WithTag()
136 checkerExceptionInstance = None
137 try:
138 varscanHit.setAttributes(lResults, lineNumber)
139 except CheckerException, e:
140 checkerExceptionInstance = e
141
142 expMessage = "The field Position is empty in varscan file in line 1"
143 obsMessage = checkerExceptionInstance.msg
144
145 self.assertEquals(expMessage, obsMessage)
146
147 def test_setAttributes_empty_ref(self):
148 lResults = ['chr1', '1000', '', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA']
149 lineNumber = 1
150
151 varscanHit = VarscanHit_WithTag()
152 checkerExceptionInstance = None
153 try:
154 varscanHit.setAttributes(lResults, lineNumber)
155 except CheckerException, e:
156 checkerExceptionInstance = e
157
158 expMessage = "The field Ref is empty in varscan file in line 1"
159 obsMessage = checkerExceptionInstance.msg
160
161 self.assertEquals(expMessage, obsMessage)
162
163 def test_setAttributes_empty_cns(self):
164 lResults = ['chr1', '1000', 'T', '', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA']
165 lineNumber = 1
166
167 varscanHit = VarscanHit_WithTag()
168 checkerExceptionInstance = None
169 try:
170 varscanHit.setAttributes(lResults, lineNumber)
171 except CheckerException, e:
172 checkerExceptionInstance = e
173
174 expMessage = "The field Var is empty in varscan file in line 1"
175 obsMessage = checkerExceptionInstance.msg
176
177 self.assertEquals(expMessage, obsMessage)
178
179 def test__eq__notEquals(self):
180 varscanHit1 = VarscanHit_WithTag()
181 varscanHit1.setChrom('C02HBa0291P19_LR48')
182 varscanHit1.setPosition('34')
183 varscanHit1.setRef('A')
184 varscanHit1.setVar('T')
185 varscanHit1.setVar('EspeceA')
186
187 varscanHit2 = VarscanHit_WithTag()
188 varscanHit2.setChrom('C02HBa0291P19_LR48')
189 varscanHit2.setPosition('34')
190 varscanHit2.setRef('A')
191 varscanHit2.setVar('T')
192 varscanHit2.setVar('EspeceB')
193
194 self.assertFalse(varscanHit1 == varscanHit2)
195
196 def test__eq__Equals(self):
197 varscanHit1 = VarscanHit_WithTag()
198 varscanHit1.setChrom('C02HBa0291P19_LR48')
199 varscanHit1.setPosition('34')
200 varscanHit1.setRef('A')
201 varscanHit1.setVar('T')
202 varscanHit1.setVar('EspeceA')
203
204 varscanHit2 = VarscanHit_WithTag()
205 varscanHit2.setChrom('C02HBa0291P19_LR48')
206 varscanHit2.setPosition('34')
207 varscanHit2.setRef('A')
208 varscanHit2.setVar('T')
209 varscanHit2.setVar('EspeceA')
210
211 if __name__ == "__main__":
212 unittest.main()