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comparison commons/core/parsing/test/Test_VarscanHit_v2_2_8_WithTag.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 import unittest
2 from commons.core.checker.CheckerException import CheckerException
3 from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag
4 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
5
6 class Test_VarscanHit_v2_2_8_WithTag(unittest.TestCase):
7
8 def test_setAttributesFromString(self):
9 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\tEspeceA\n"
10
11 expChrom = "chr1"
12 expPosition = "1804"
13 expRef = "T"
14 expCns = "C"
15 expReadsRef = "0"
16 expReadsVar = "1"
17 expVarFreq = "100%"
18 expStrandsRef = "0"
19 expStrandsVar = "1"
20 expQualRef = "0"
21 expQualVar = "53"
22 expPValue = "0.98"
23 expMapQualRef = "0"
24 expMapQualVar = "1"
25 expReadsRefPlus = "0"
26 expReadsRefMinus = "0"
27 expReadsVarPlus = "1"
28 expReadsVarMinus = "0"
29 expVar = "C"
30 expTag = "EspeceA"
31
32 varscanHit = VarscanHit_v2_2_8_WithTag()
33 varscanHit.setAttributesFromString(line)
34
35 obsChrom = varscanHit.getChrom()
36 obsPosition = varscanHit.getPosition()
37 obsRef = varscanHit.getRef()
38 obsCns = varscanHit.getCns()
39 obsReadsRef = varscanHit.getReadsRef()
40 obsReadsVar = varscanHit.getReadsVar()
41 obsVarFreq = varscanHit.getVarFreq()
42 obsStrandsRef = varscanHit.getStrandsRef()
43 obsStrandsVar = varscanHit.getStrandsVar()
44 obsQualRef = varscanHit.getQualRef()
45 obsQualVar = varscanHit.getQualVar()
46 obsPValue = varscanHit.getPValue()
47 obsMapQualRef = varscanHit.getMapQualRef()
48 obsMapQualVar = varscanHit.getMapQualVar()
49 obsReadsRefPlus = varscanHit.getReadsRefPlus()
50 obsReadsRefMinus = varscanHit.getReadsRefMinus()
51 obsReadsVarPlus = varscanHit.getReadsVarPlus()
52 obsReadsVarMinus = varscanHit.getReadsVarMinus()
53 obsVar = varscanHit.getVar()
54 obsTag = varscanHit.getTag()
55
56 self.assertEquals(expChrom, obsChrom)
57 self.assertEquals(expPosition, obsPosition)
58 self.assertEquals(expRef, obsRef)
59 self.assertEquals(expCns, obsCns)
60 self.assertEquals(expReadsRef, obsReadsRef)
61 self.assertEquals(expReadsVar, obsReadsVar)
62 self.assertEquals(expVarFreq, obsVarFreq)
63 self.assertEquals(expStrandsRef, obsStrandsRef)
64 self.assertEquals(expStrandsVar, obsStrandsVar)
65 self.assertEquals(expQualRef, obsQualRef)
66 self.assertEquals(expQualVar, obsQualVar)
67 self.assertEquals(expPValue, obsPValue)
68 self.assertEquals(expMapQualRef, obsMapQualRef)
69 self.assertEquals(expMapQualVar, obsMapQualVar)
70 self.assertEquals(expReadsRefPlus, obsReadsRefPlus)
71 self.assertEquals(expReadsRefMinus, obsReadsRefMinus)
72 self.assertEquals(expReadsVarPlus, obsReadsVarPlus)
73 self.assertEquals(expReadsVarMinus, obsReadsVarMinus)
74 self.assertEquals(expVar, obsVar)
75 self.assertEquals(expTag, obsTag)
76
77 def test_setAttributesFromString_empty_chrom(self):
78 line = "\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\tEspeceA\n"
79 varscanHit = VarscanHit_v2_2_8_WithTag()
80 try :
81 varscanHit.setAttributesFromString(line)
82 except CheckerException, e:
83 checkerExceptionInstance = e
84 expMessage = "The field Chrom is empty in varscan file in line "
85 obsMessage = checkerExceptionInstance.msg
86 self.assertEquals(expMessage, obsMessage)
87
88 def test_setAttributesFromString_less_than_20_fields(self):
89 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\tEspeceA\n"
90 varscanHit = VarscanHit_v2_2_8_WithTag()
91 try :
92 varscanHit.setAttributesFromString(line)
93 except CheckerException, e:
94 checkerExceptionInstance = e
95 expMessage = "This varscan line (l.) is not complete"
96 obsMessage = checkerExceptionInstance.msg
97 self.assertEquals(expMessage, obsMessage)
98
99 def test_setAttributes(self):
100 lResults = ['chr1', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
101 lineNumber = 1
102
103 expChrom = "chr1"
104 expPosition = "1804"
105 expRef = "T"
106 expCns = "C"
107 expReadsRef = "0"
108 expReadsVar = "1"
109 expVarFreq = "100%"
110 expStrandsRef = "0"
111 expStrandsVar = "1"
112 expQualRef = "0"
113 expQualVar = "53"
114 expPValue = "0.98"
115 expMapQualRef = "0"
116 expMapQualVar = "1"
117 expReadsRefPlus = "0"
118 expReadsRefMinus = "0"
119 expReadsVarPlus = "1"
120 expReadsVarMinus = "0"
121 expVar = "C"
122 expTag = "EspeceA"
123
124 varscanHit = VarscanHit_v2_2_8_WithTag()
125 varscanHit.setAttributes(lResults, lineNumber)
126
127 obsChrom = varscanHit.getChrom()
128 obsPosition = varscanHit.getPosition()
129 obsRef = varscanHit.getRef()
130 obsCns = varscanHit.getCns()
131 obsReadsRef = varscanHit.getReadsRef()
132 obsReadsVar = varscanHit.getReadsVar()
133 obsVarFreq = varscanHit.getVarFreq()
134 obsStrandsRef = varscanHit.getStrandsRef()
135 obsStrandsVar = varscanHit.getStrandsVar()
136 obsQualRef = varscanHit.getQualRef()
137 obsQualVar = varscanHit.getQualVar()
138 obsPValue = varscanHit.getPValue()
139 obsMapQualRef = varscanHit.getMapQualRef()
140 obsMapQualVar = varscanHit.getMapQualVar()
141 obsReadsRefPlus = varscanHit.getReadsRefPlus()
142 obsReadsRefMinus = varscanHit.getReadsRefMinus()
143 obsReadsVarPlus = varscanHit.getReadsVarPlus()
144 obsReadsVarMinus = varscanHit.getReadsVarMinus()
145 obsVar = varscanHit.getVar()
146 obsTag = varscanHit.getTag()
147
148 self.assertEquals(expChrom, obsChrom)
149 self.assertEquals(expPosition, obsPosition)
150 self.assertEquals(expRef, obsRef)
151 self.assertEquals(expCns, obsCns)
152 self.assertEquals(expReadsRef, obsReadsRef)
153 self.assertEquals(expReadsVar, obsReadsVar)
154 self.assertEquals(expVarFreq, obsVarFreq)
155 self.assertEquals(expStrandsRef, obsStrandsRef)
156 self.assertEquals(expStrandsVar, obsStrandsVar)
157 self.assertEquals(expQualRef, obsQualRef)
158 self.assertEquals(expQualVar, obsQualVar)
159 self.assertEquals(expPValue, obsPValue)
160 self.assertEquals(expMapQualRef, obsMapQualRef)
161 self.assertEquals(expMapQualVar, obsMapQualVar)
162 self.assertEquals(expReadsRefPlus, obsReadsRefPlus)
163 self.assertEquals(expReadsRefMinus, obsReadsRefMinus)
164 self.assertEquals(expReadsVarPlus, obsReadsVarPlus)
165 self.assertEquals(expReadsVarMinus, obsReadsVarMinus)
166 self.assertEquals(expVar, obsVar)
167 self.assertEquals(expTag, obsTag)
168
169 def test_setAttributes_empty_chrom(self):
170 lResults = ['', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
171 lineNumber = 1
172
173 varscanHit = VarscanHit_v2_2_8_WithTag()
174 checkerExceptionInstance = None
175 try:
176 varscanHit.setAttributes(lResults, lineNumber)
177 except CheckerException, e:
178 checkerExceptionInstance = e
179
180 expMessage = "The field Chrom is empty in varscan file in line 1"
181 obsMessage = checkerExceptionInstance.msg
182
183 self.assertEquals(expMessage, obsMessage)
184
185 def test_setAttributes_empty_position(self):
186 lResults = ['chr1', '', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
187 lineNumber = 1
188
189 varscanHit = VarscanHit_v2_2_8_WithTag()
190 checkerExceptionInstance = None
191 try:
192 varscanHit.setAttributes(lResults, lineNumber)
193 except CheckerException, e:
194 checkerExceptionInstance = e
195
196 expMessage = "The field Position is empty in varscan file in line 1"
197 obsMessage = checkerExceptionInstance.msg
198
199 self.assertEquals(expMessage, obsMessage)
200
201 def test_setAttributes_empty_ref(self):
202 lResults = ['chr1', '1000', '', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
203 lineNumber = 1
204
205 varscanHit = VarscanHit_v2_2_8_WithTag()
206 checkerExceptionInstance = None
207 try:
208 varscanHit.setAttributes(lResults, lineNumber)
209 except CheckerException, e:
210 checkerExceptionInstance = e
211
212 expMessage = "The field Ref is empty in varscan file in line 1"
213 obsMessage = checkerExceptionInstance.msg
214
215 self.assertEquals(expMessage, obsMessage)
216
217 def test_setAttributes_empty_cns(self):
218 lResults = ['chr1', '1000', 'T', '', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C', 'EspeceA']
219 lineNumber = 1
220
221 varscanHit = VarscanHit_v2_2_8_WithTag()
222 checkerExceptionInstance = None
223 try:
224 varscanHit.setAttributes(lResults, lineNumber)
225 except CheckerException, e:
226 checkerExceptionInstance = e
227
228 expMessage = "The field Cons is empty in varscan file in line 1"
229 obsMessage = checkerExceptionInstance.msg
230
231 self.assertEquals(expMessage, obsMessage)
232
233 def test_setAttributes_empty_var(self):
234 lResults = ['chr1', '1000', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', '', 'EspeceA']
235 lineNumber = 1
236
237 varscanHit = VarscanHit_v2_2_8_WithTag()
238 checkerExceptionInstance = None
239 try:
240 varscanHit.setAttributes(lResults, lineNumber)
241 except CheckerException, e:
242 checkerExceptionInstance = e
243
244 expMessage = "The field varAllele is empty in varscan file in line 1"
245 obsMessage = checkerExceptionInstance.msg
246
247 self.assertEquals(expMessage, obsMessage)
248
249 def test__eq__notEquals(self):
250 varscanHit1 = VarscanHit_v2_2_8_WithTag()
251 varscanHit1.setChrom('C02HBa0291P19_LR48')
252 varscanHit1.setPosition('34')
253 varscanHit1.setRef('A')
254 varscanHit1.setCns('T')
255 varscanHit1.setVar('T')
256 varscanHit1.setVar('EspeceA')
257
258 varscanHit2 = VarscanHit_v2_2_8_WithTag()
259 varscanHit2.setChrom('C02HBa0291P19_LR48')
260 varscanHit2.setPosition('34')
261 varscanHit2.setRef('A')
262 varscanHit2.setCns('T')
263 varscanHit2.setVar('T')
264 varscanHit2.setVar('EspeceB')
265
266 self.assertFalse(varscanHit1 == varscanHit2)
267
268 def test__eq__Equals(self):
269 varscanHit1 = VarscanHit_v2_2_8_WithTag()
270 varscanHit1.setChrom('C02HBa0291P19_LR48')
271 varscanHit1.setPosition('34')
272 varscanHit1.setRef('A')
273 varscanHit1.setCns('T')
274 varscanHit1.setVar('T')
275 varscanHit1.setVar('EspeceA')
276
277 varscanHit2 = VarscanHit_v2_2_8_WithTag()
278 varscanHit2.setChrom('C02HBa0291P19_LR48')
279 varscanHit2.setPosition('34')
280 varscanHit2.setRef('A')
281 varscanHit2.setCns('T')
282 varscanHit2.setVar('T')
283 varscanHit2.setVar('EspeceA')
284
285 self.assertTrue(varscanHit1 == varscanHit2)
286
287 def test_convertVarscanHit_v2_2_8_WithTag_To_VarscanHit_WithTag(self):
288 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\tEspeceA\n"
289 iVarscanHit_v2_2_8_WithTag = VarscanHit_v2_2_8_WithTag()
290 iVarscanHit_v2_2_8_WithTag.setAttributesFromString(line)
291 obsVarcanHit_WithTag = iVarscanHit_v2_2_8_WithTag.convertVarscanHit_v2_2_8_WithTag_To_VarscanHit_WithTag()
292
293 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\tEspeceA\n"
294 expVarcanHit_WithTag = VarscanHit_WithTag()
295 expVarcanHit_WithTag.setAttributesFromString(line)
296
297 self.assertEquals(expVarcanHit_WithTag, obsVarcanHit_WithTag)
298
299 if __name__ == "__main__":
300 unittest.main()