Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/test/Test_VarscanHitForGnpSNP.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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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() |