6
|
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() |