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comparison commons/core/parsing/test/Test_VarscanHitForGnpSNP.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.parsing.VarscanHitForGnpSNP import VarscanHitForGnpSNP
3 from commons.core.checker.CheckerException import CheckerException
4
5 class Test_VarscanHitForGnpSNP(unittest.TestCase):
6
7 def test_setAttributes(self):
8 lResults = ["C02HBa0291P19_LR48", "32", "C", "T", "1", "2", "66,67%", "1", "1", "37", "35", "0.3999999999999999"]
9 lineNumber = 1
10
11 expChrom = "C02HBa0291P19_LR48"
12 expPosition = "32"
13 expRef = "C"
14 expVar = "T"
15 expReads1 = "1"
16 expReads2 = "2"
17 expVarFreq = 66.67
18 expStrands1 = "1"
19 expStrands2 = "1"
20 expQual1 = "37"
21 expQual2 = "35"
22 expPvalue = "0.3999999999999999"
23
24 varscanHit = VarscanHitForGnpSNP()
25 varscanHit.setAttributes(lResults, lineNumber)
26
27 obsChrom = varscanHit.getChrom()
28 obsPosition = varscanHit.getPosition()
29 obsRef = varscanHit.getRef()
30 obsVar = varscanHit.getVar()
31 obsReads1 = varscanHit.getReads1()
32 obsReads2 = varscanHit.getReads2()
33 obsVarFreq = varscanHit.getVarFreq()
34 obsStrands1 = varscanHit.getStrands1()
35 obsStrands2 = varscanHit.getStrands2()
36 obsQual1 = varscanHit.getQual1()
37 obsQual2 = varscanHit.getQual2()
38 obsPvalue = varscanHit.getPvalue()
39
40 self.assertEquals(expChrom, obsChrom)
41 self.assertEquals(expPosition, obsPosition)
42 self.assertEquals(expRef, obsRef)
43 self.assertEquals(expVar, obsVar)
44 self.assertEquals(expReads1, obsReads1)
45 self.assertEquals(expReads2, obsReads2)
46 self.assertEquals(expVarFreq, obsVarFreq)
47 self.assertEquals(expStrands1, obsStrands1)
48 self.assertEquals(expStrands2, obsStrands2)
49 self.assertEquals(expQual1, obsQual1)
50 self.assertEquals(expQual2, obsQual2)
51 self.assertEquals(expPvalue, obsPvalue)
52
53 def test_setAttributes_empty_chrom(self):
54 lResults = ["", "", "", "", "", "", "10", "", "", "", "", ""]
55 lineNumber = 1
56
57 varscanHit = VarscanHitForGnpSNP()
58 checkerExceptionInstance = None
59 try:
60 varscanHit.setAttributes(lResults, lineNumber)
61 except CheckerException, e:
62 checkerExceptionInstance = e
63
64 expMessage = "The field Chrom is empty in varscan file in line 1"
65 obsMessage = checkerExceptionInstance.msg
66
67 self.assertEquals(expMessage, obsMessage)
68
69 def test_setAttributes_empty_position(self):
70 lResults = ["chrom", "", "", "", "", "", "10", "", "", "", "", ""]
71 lineNumber = 5
72
73 varscanHit = VarscanHitForGnpSNP()
74 checkerExceptionInstance = None
75 try:
76 varscanHit.setAttributes(lResults, lineNumber)
77 except CheckerException, e:
78 checkerExceptionInstance = e
79
80 expMessage = "The field Position is empty in varscan file in line 5"
81 obsMessage = checkerExceptionInstance.msg
82
83 self.assertEquals(expMessage, obsMessage)
84
85 def test_setAttributes_empty_ref(self):
86 lResults = ["chrom", "position", "", "", "", "", "10", "", "", "", "", ""]
87 lineNumber = 5
88
89 varscanHit = VarscanHitForGnpSNP()
90 checkerExceptionInstance = None
91 try:
92 varscanHit.setAttributes(lResults, lineNumber)
93 except CheckerException, e:
94 checkerExceptionInstance = e
95
96 expMessage = "The field Ref is empty in varscan file in line 5"
97 obsMessage = checkerExceptionInstance.msg
98
99 self.assertEquals(expMessage, obsMessage)
100
101 def test_setAttributes_empty_var(self):
102 lResults = ["chrom", "position", "ref", "", "", "", "10", "", "", "", "", ""]
103 lineNumber = 5
104
105 varscanHit = VarscanHitForGnpSNP()
106 checkerExceptionInstance = None
107 try:
108 varscanHit.setAttributes(lResults, lineNumber)
109 except CheckerException, e:
110 checkerExceptionInstance = e
111
112 expMessage = "The field Var is empty in varscan file in line 5"
113 obsMessage = checkerExceptionInstance.msg
114
115 self.assertEquals(expMessage, obsMessage)
116
117 def test_setAttributes_empty_reads1(self):
118 lResults = ["chrom", "position", "ref", "var", "", "", "10", "", "", "", "", ""]
119 lineNumber = 5
120
121 varscanHit = VarscanHitForGnpSNP()
122 checkerExceptionInstance = None
123 try:
124 varscanHit.setAttributes(lResults, lineNumber)
125 except CheckerException, e:
126 checkerExceptionInstance = e
127
128 expMessage = "The field Reads1 is empty in varscan file in line 5"
129 obsMessage = checkerExceptionInstance.msg
130
131 self.assertEquals(expMessage, obsMessage)
132
133 def test_setAttributes_empty_reads2(self):
134 lResults = ["chrom", "position", "ref", "var", "reads1", "", "10", "", "", "", "", ""]
135 lineNumber = 5
136
137 varscanHit = VarscanHitForGnpSNP()
138 checkerExceptionInstance = None
139 try:
140 varscanHit.setAttributes(lResults, lineNumber)
141 except CheckerException, e:
142 checkerExceptionInstance = e
143
144 expMessage = "The field Reads2 is empty in varscan file in line 5"
145 obsMessage = checkerExceptionInstance.msg
146
147 self.assertEquals(expMessage, obsMessage)
148
149 def test_setAttributes_empty_varFreq(self):
150 lResults = ["chrom", "position", "ref", "var", "reads1", "reads2", "", "", "", "", "", ""]
151 lineNumber = 5
152
153 varscanHit = VarscanHitForGnpSNP()
154 checkerExceptionInstance = None
155 try:
156 varscanHit.setAttributes(lResults, lineNumber)
157 except CheckerException, e:
158 checkerExceptionInstance = e
159
160 expMessage = "The field VarFreq is empty or in bad format in varscan file in line 5"
161 obsMessage = checkerExceptionInstance.msg
162
163 self.assertEquals(expMessage, obsMessage)
164
165 def test_setAttributes_empty_strands1(self):
166 lResults = ["chrom", "position", "ref", "var", "reads1", "reads2", "10", "", "", "", "", ""]
167 lineNumber = 5
168
169 varscanHit = VarscanHitForGnpSNP()
170 checkerExceptionInstance = None
171 try:
172 varscanHit.setAttributes(lResults, lineNumber)
173 except CheckerException, e:
174 checkerExceptionInstance = e
175
176 expMessage = "The field Strands1 is empty in varscan file in line 5"
177 obsMessage = checkerExceptionInstance.msg
178
179 self.assertEquals(expMessage, obsMessage)
180
181 def test_setAttributes_empty_strands2(self):
182 lResults = ["chrom", "position", "ref", "var", "reads1", "reads2", "10", "strands1", "", "", "", ""]
183 lineNumber = 5
184
185 varscanHit = VarscanHitForGnpSNP()
186 checkerExceptionInstance = None
187 try:
188 varscanHit.setAttributes(lResults, lineNumber)
189 except CheckerException, e:
190 checkerExceptionInstance = e
191
192 expMessage = "The field Strands2 is empty in varscan file in line 5"
193 obsMessage = checkerExceptionInstance.msg
194
195 self.assertEquals(expMessage, obsMessage)
196
197 def test_setAttributes_empty_qual1(self):
198 lResults = ["chrom", "position", "ref", "var", "reads1", "reads2", "10", "strands1", "strands2", "", "", ""]
199 lineNumber = 5
200
201 varscanHit = VarscanHitForGnpSNP()
202 checkerExceptionInstance = None
203 try:
204 varscanHit.setAttributes(lResults, lineNumber)
205 except CheckerException, e:
206 checkerExceptionInstance = e
207
208 expMessage = "The field Qual1 is empty in varscan file in line 5"
209 obsMessage = checkerExceptionInstance.msg
210
211 self.assertEquals(expMessage, obsMessage)
212
213 def test_setAttributes_empty_qual2(self):
214 lResults = ["chrom", "position", "ref", "var", "reads1", "reads2", "10", "strands1", "strands2", "qual1", "", ""]
215 lineNumber = 5
216
217 varscanHit = VarscanHitForGnpSNP()
218 checkerExceptionInstance = None
219 try:
220 varscanHit.setAttributes(lResults, lineNumber)
221 except CheckerException, e:
222 checkerExceptionInstance = e
223
224 expMessage = "The field Qual2 is empty in varscan file in line 5"
225 obsMessage = checkerExceptionInstance.msg
226
227 self.assertEquals(expMessage, obsMessage)
228
229 def test_setAttributes_empty_pvalue(self):
230 lResults = ["chrom", "position", "ref", "var", "reads1", "reads2", "10", "strands1", "strands2", "qual1", "qual2", ""]
231 lineNumber = 5
232
233 varscanHit = VarscanHitForGnpSNP()
234 checkerExceptionInstance = None
235 try:
236 varscanHit.setAttributes(lResults, lineNumber)
237 except CheckerException, e:
238 checkerExceptionInstance = e
239
240 expMessage = "The field Pvalue is empty in varscan file in line 5"
241 obsMessage = checkerExceptionInstance.msg
242
243 self.assertEquals(expMessage, obsMessage)
244
245 def test__eq__notEquals(self):
246 varscanHit1 = VarscanHitForGnpSNP()
247 varscanHit1.setChrom('C02HBa0291P19_LR48')
248 varscanHit1.setPosition('32')
249 varscanHit1.setRef('C')
250 varscanHit1.setVar('T')
251 varscanHit1.setReads1('1')
252 varscanHit1.setReads2('2')
253 varscanHit1.setVarFreq('66,67%')
254 varscanHit1.setStrands1('1')
255 varscanHit1.setStrands2('1')
256 varscanHit1.setQual1('37')
257 varscanHit1.setQual2('35')
258 varscanHit1.setPvalue('0.3999999999999999')
259
260 varscanHit2 = VarscanHitForGnpSNP()
261 varscanHit2.setChrom('C02HBa0291P19_LR48')
262 varscanHit2.setPosition('34')
263 varscanHit2.setRef('A')
264 varscanHit2.setVar('T')
265 varscanHit2.setReads1('1')
266 varscanHit2.setReads2('2')
267 varscanHit2.setVarFreq('66,67%')
268 varscanHit2.setStrands1('1')
269 varscanHit2.setStrands2('1')
270 varscanHit2.setQual1('40')
271 varscanHit2.setQual2('34')
272 varscanHit2.setPvalue('0.3999999999999999')
273
274 self.assertFalse(varscanHit1 == varscanHit2)
275
276 def test__eq__Equals(self):
277 varscanHit1 = VarscanHitForGnpSNP()
278 varscanHit1.setChrom('C02HBa0291P19_LR48')
279 varscanHit1.setPosition('32')
280 varscanHit1.setRef('C')
281 varscanHit1.setVar('T')
282 varscanHit1.setReads1('1')
283 varscanHit1.setReads2('2')
284 varscanHit1.setVarFreq('66,67%')
285 varscanHit1.setStrands1('1')
286 varscanHit1.setStrands2('1')
287 varscanHit1.setQual1('37')
288 varscanHit1.setQual2('35')
289 varscanHit1.setPvalue('0.3999999999999999')
290
291 varscanHit2 = VarscanHitForGnpSNP()
292 varscanHit2.setChrom('C02HBa0291P19_LR48')
293 varscanHit2.setPosition('32')
294 varscanHit2.setRef('C')
295 varscanHit2.setVar('T')
296 varscanHit2.setReads1('1')
297 varscanHit2.setReads2('2')
298 varscanHit2.setVarFreq('66,67%')
299 varscanHit2.setStrands1('1')
300 varscanHit2.setStrands2('1')
301 varscanHit2.setQual1('37')
302 varscanHit2.setQual2('35')
303 varscanHit2.setPvalue('0.3999999999999999')
304
305 self.assertTrue(varscanHit1 == varscanHit2)
306
307 def test_formatAlleles2GnpSnp_for_Deletion(self):
308 varscanHit1 = VarscanHitForGnpSNP()
309 varscanHit1.setChrom('C02HBa0291P19_LR48')
310 varscanHit1.setPosition('32')
311 varscanHit1.setRef('C')
312 varscanHit1.setVar('-ATT')
313 varscanHit1.setReads1('1')
314 varscanHit1.setReads2('2')
315 varscanHit1.setVarFreq('66,67%')
316 varscanHit1.setStrands1('1')
317 varscanHit1.setStrands2('1')
318 varscanHit1.setQual1('37')
319 varscanHit1.setQual2('35')
320 varscanHit1.setPvalue('0.3999999999999999')
321
322 expPolymType = "DELETION"
323 expGnpSnpRef = "ATT"
324 expGnpSnpVar = "---"
325 expGnpSnpPosition = 33
326
327 varscanHit1.formatAlleles2GnpSnp()
328
329 obsPolymType = varscanHit1.getPolymType()
330 obsGnpSnpRef = varscanHit1.getGnpSnpRef()
331 obsGnpSnpVar = varscanHit1.getGnpSnpVar()
332 obsGnpSnpPosition = varscanHit1.getGnpSnpPosition()
333
334 self.assertEquals(expPolymType,obsPolymType)
335 self.assertEquals(expGnpSnpRef, obsGnpSnpRef)
336 self.assertEquals(expGnpSnpVar, obsGnpSnpVar)
337 self.assertEquals(expGnpSnpPosition, obsGnpSnpPosition)
338
339 def test_setVarFreq(self):
340 varscanHit1 = VarscanHitForGnpSNP()
341 exp = 66.67
342 varscanHit1.setVarFreq('66,67%')
343 obs = varscanHit1.getVarFreq()
344 self.assertEquals(exp, obs)
345
346 def test_formatAlleles2GnpSnp_for_Insertion(self):
347 varscanHit1 = VarscanHitForGnpSNP()
348 varscanHit1.setChrom('C02HBa0291P19_LR48')
349 varscanHit1.setPosition('32')
350 varscanHit1.setRef('C')
351 varscanHit1.setVar('+TG')
352 varscanHit1.setReads1('1')
353 varscanHit1.setReads2('2')
354 varscanHit1.setVarFreq('66,67%')
355 varscanHit1.setStrands1('1')
356 varscanHit1.setStrands2('1')
357 varscanHit1.setQual1('37')
358 varscanHit1.setQual2('35')
359 varscanHit1.setPvalue('0.3999999999999999')
360
361 expPolymType = "INSERTION"
362 expGnpSnpRef = "--"
363 expGnpSnpVar = "TG"
364 expGnpSnpPosition = 32
365
366 varscanHit1.formatAlleles2GnpSnp()
367
368 obsPolymType = varscanHit1.getPolymType()
369 obsGnpSnpRef = varscanHit1.getGnpSnpRef()
370 obsGnpSnpVar = varscanHit1.getGnpSnpVar()
371 obsGnpSnpPosition = varscanHit1.getGnpSnpPosition()
372
373 self.assertEquals(expPolymType,obsPolymType)
374 self.assertEquals(expGnpSnpRef, obsGnpSnpRef)
375 self.assertEquals(expGnpSnpVar, obsGnpSnpVar)
376 self.assertEquals(expGnpSnpPosition, obsGnpSnpPosition)
377
378 def test_formatAlleles2GnpSnp_for_SNP(self):
379 varscanHit1 = VarscanHitForGnpSNP()
380 varscanHit1.setChrom('C02HBa0291P19_LR48')
381 varscanHit1.setPosition('12')
382 varscanHit1.setRef('G')
383 varscanHit1.setVar('T')
384 varscanHit1.setReads1('1')
385 varscanHit1.setReads2('2')
386 varscanHit1.setVarFreq('66,67%')
387 varscanHit1.setStrands1('1')
388 varscanHit1.setStrands2('1')
389 varscanHit1.setQual1('37')
390 varscanHit1.setQual2('35')
391 varscanHit1.setPvalue('0.3999999999999999')
392
393 expPolymType = "SNP"
394 expGnpSnpRef = "G"
395 expGnpSnpVar = "T"
396 expGnpSnpPosition = 12
397
398 varscanHit1.formatAlleles2GnpSnp()
399
400 obsPolymType = varscanHit1.getPolymType()
401 obsGnpSnpRef = varscanHit1.getGnpSnpRef()
402 obsGnpSnpVar = varscanHit1.getGnpSnpVar()
403 obsGnpSnpPosition = varscanHit1.getGnpSnpPosition()
404
405 self.assertEquals(expPolymType,obsPolymType)
406 self.assertEquals(expGnpSnpRef, obsGnpSnpRef)
407 self.assertEquals(expGnpSnpVar, obsGnpSnpVar)
408 self.assertEquals(expGnpSnpPosition, obsGnpSnpPosition)
409
410
411 if __name__ == "__main__":
412 unittest.main()