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comparison commons/core/parsing/test/Test_VarscanFile.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 from commons.core.parsing.VarscanFile import VarscanFile
2 from commons.core.parsing.VarscanHit import VarscanHit
3 import unittest
4 import os
5 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
6 from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8
7 from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag
8 from commons.core.checker.CheckerException import CheckerException
9
10 class Test_VarscanFile(unittest.TestCase):
11
12 def test_parse_fileWithHeader(self):
13 varscanFileName = "file.varscan"
14 self._writeVarscanFile(varscanFileName)
15
16 varscanHit1 = VarscanHit()
17 varscanHit1.setChrom('C02HBa0291P19_LR48')
18 varscanHit1.setPosition('32')
19 varscanHit1.setRef('C')
20 varscanHit1.setVar('T')
21
22 varscanHit2 = VarscanHit()
23 varscanHit2.setChrom('C02HBa0291P19_LR48')
24 varscanHit2.setPosition('34')
25 varscanHit2.setRef('A')
26 varscanHit2.setVar('T')
27 expVarscanHitsList = [varscanHit1, varscanHit2]
28
29 iVarscanFile = VarscanFile(varscanFileName)
30 iVarscanFile.parse()
31 obsVarscanHitsList = iVarscanFile.getVarscanHitsList()
32 os.remove(varscanFileName)
33
34 self.assertEquals(expVarscanHitsList, obsVarscanHitsList)
35
36 def test_parse_FileWithoutHeader(self):
37 varscanFileName = "file.varscan"
38 self._writeVarscanFileWithoutHeader(varscanFileName)
39
40 varscanHit1 = VarscanHit()
41 varscanHit1.setChrom('C02HBa0291P19_LR48')
42 varscanHit1.setPosition('32')
43 varscanHit1.setRef('C')
44 varscanHit1.setVar('T')
45
46 varscanHit2 = VarscanHit()
47 varscanHit2.setChrom('C02HBa0291P19_LR48')
48 varscanHit2.setPosition('34')
49 varscanHit2.setRef('A')
50 varscanHit2.setVar('T')
51 expVarscanHitsList = [varscanHit1, varscanHit2]
52
53 iVarscanFile = VarscanFile(varscanFileName)
54 iVarscanFile.parse()
55 obsVarscanHitsList = iVarscanFile.getVarscanHitsList()
56 obsTypeOfVarscanFile = iVarscanFile.getTypeOfVarscanFile()
57 expTypeOfVarscanFile = "Varscan_2_2"
58
59 self.assertEquals(expVarscanHitsList, obsVarscanHitsList)
60 self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile)
61 os.remove(varscanFileName)
62
63 def test_parse_VarscanFileWithTag(self):
64 inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
65 self._writeVarscanFileWithTag(inputFileName)
66 launcher = VarscanFile(inputFileName)
67 launcher.parse()
68 obsListOfVarscanHits = launcher.getListOfVarscanHits()
69
70 varscanHit1 = VarscanHit_WithTag()
71 varscanHit1.setChrom('C02HBa0291P19_LR48')
72 varscanHit1.setPosition('32')
73 varscanHit1.setRef('C')
74 varscanHit1.setVar('T')
75 varscanHit1.setTag('EspeceA')
76
77 varscanHit2 = VarscanHit_WithTag()
78 varscanHit2.setChrom('C02HBa0291P19_LR48')
79 varscanHit2.setPosition('34')
80 varscanHit2.setRef('A')
81 varscanHit2.setVar('T')
82 varscanHit2.setTag('EspeceA')
83 expVarscanHitsList = [varscanHit1, varscanHit2]
84
85 obsTypeOfVarscanFile = launcher.getTypeOfVarscanFile()
86 expTypeOfVarscanFile = "Varscan_2_2_WithTag"
87
88 self.assertEquals(expVarscanHitsList, obsListOfVarscanHits)
89 self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile)
90 os.remove(inputFileName)
91
92 def test_parse_VarscanFile_v2_2_8(self):
93 inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
94 self._writeVarscanFile_v2_2_8(inputFileName)
95 launcher = VarscanFile(inputFileName)
96 launcher.parse()
97 obsListOfVarscanHits = launcher.getListOfVarscanHits()
98
99 varscanHit1 = VarscanHit_v2_2_8()
100 varscanHit1.setChrom('C11HBa0064J13_LR285')
101 varscanHit1.setPosition('3227')
102 varscanHit1.setRef('G')
103 varscanHit1.setVar('A')
104 varscanHit1.setCns('A')
105
106 varscanHit2 = VarscanHit_v2_2_8()
107 varscanHit2.setChrom('C11HBa0064J13_LR285')
108 varscanHit2.setPosition('3230')
109 varscanHit2.setRef('G')
110 varscanHit2.setVar('T')
111 varscanHit2.setCns('T')
112 expVarscanHitsList = [varscanHit1, varscanHit2]
113
114 obsTypeOfVarscanFile = launcher.getTypeOfVarscanFile()
115 expTypeOfVarscanFile = "Varscan_2_2_8"
116
117 self.assertEquals(expVarscanHitsList, obsListOfVarscanHits)
118 self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile)
119 os.remove(inputFileName)
120
121 def test_parse_other(self):
122 inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
123 self._writeOther(inputFileName)
124 launcher = VarscanFile(inputFileName)
125 try:
126 launcher.parse()
127 except CheckerException, e:
128 checkerExceptionInstance = e
129 expMessage = "Warning: this line (l.1) is not a valid varscan line !"
130 obsMessage = checkerExceptionInstance.msg
131 os.remove(inputFileName)
132 self.assertEquals(expMessage, obsMessage)
133
134 def test__eq__notEqual(self):
135 lVarscanHits1 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
136 iVarscanFile1 = VarscanFile()
137 iVarscanFile1.setVarscanHitsList(lVarscanHits1)
138 lVarscanHits2 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "C")]
139 iVarscanFile2 = VarscanFile()
140 iVarscanFile2.setVarscanHitsList(lVarscanHits2)
141
142 self.assertNotEquals(iVarscanFile1, iVarscanFile2)
143
144 def test__eq__equal(self):
145 lVarscanHits1 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
146 iVarscanFile1 = VarscanFile()
147 iVarscanFile1.setVarscanHitsList(lVarscanHits1)
148 lVarscanHits2 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
149 iVarscanFile2 = VarscanFile()
150 iVarscanFile2.setVarscanHitsList(lVarscanHits2)
151
152 self.assertEquals(iVarscanFile1, iVarscanFile2)
153
154 def test_selectTypeOfVarscanHitObject_noVarscanHit(self):
155 launcher = VarscanFile()
156 launcher.setTypeOfVarscanFile("")
157 try:
158 launcher.selectTypeOfVarscanHitObject()
159 except CheckerException, e:
160 checkerExceptionInstance = e
161 expMessage = "Error: no varscan object found !"
162 obsMessage = checkerExceptionInstance.msg
163 self.assertEquals(expMessage, obsMessage)
164
165 def test_selectTypeOfVarscanHitObject_VarscanHit(self):
166 launcher = VarscanFile()
167 launcher.setTypeOfVarscanFile("Varscan_2_2")
168 obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
169 expVarscanHit = VarscanHit()
170 self.assertEquals(expVarscanHit, obsVarscanHit)
171
172 def test_selectTypeOfVarscanHitObject_VarscanHitWithTag(self):
173 launcher = VarscanFile()
174 launcher.setTypeOfVarscanFile("Varscan_2_2_WithTag")
175 obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
176 expVarscanHit = VarscanHit_WithTag()
177 self.assertEquals(expVarscanHit, obsVarscanHit)
178
179 def test_selectTypeOfVarscanHitObject_noVarscanHit_2_2_8(self):
180 launcher = VarscanFile()
181 launcher.setTypeOfVarscanFile("Varscan_2_2_8")
182 obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
183 expVarscanHit = VarscanHit_v2_2_8()
184 self.assertEquals(expVarscanHit, obsVarscanHit)
185
186 def test_selectTypeOfVarscanHitObject_noVarscanHit_2_2_8_WithTag(self):
187 launcher = VarscanFile()
188 launcher.setTypeOfVarscanFile("Varscan_2_2_8_WithTag")
189 obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
190 expVarscanHit = VarscanHit_v2_2_8_WithTag()
191 self.assertEquals(expVarscanHit, obsVarscanHit)
192
193 def test_createVarscanObjectFromLine_VarscanHit(self):
194 line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n"
195 nbLine = 1
196 launcher = VarscanFile()
197 launcher.setTypeOfVarscanFile("Varscan_2_2")
198 obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
199 expVarscanHit = VarscanHit()
200 expVarscanHit.setChrom('C02HBa0291P19_LR48')
201 expVarscanHit.setPosition('32')
202 expVarscanHit.setRef('C')
203 expVarscanHit.setVar('T')
204 self.assertEquals(expVarscanHit, obsVarscanHit)
205
206 def test_createVarscanObjectFromLine_VarscanHitWithTag(self):
207 line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\tEspeceA\n"
208 nbLine = 1
209 launcher = VarscanFile()
210 launcher.setTypeOfVarscanFile("Varscan_2_2_WithTag")
211 obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
212 expVarscanHit = VarscanHit_WithTag()
213 expVarscanHit.setChrom('C02HBa0291P19_LR48')
214 expVarscanHit.setPosition('32')
215 expVarscanHit.setRef('C')
216 expVarscanHit.setVar('T')
217 expVarscanHit.setTag('EspeceA')
218 self.assertEquals(expVarscanHit, obsVarscanHit)
219
220 def test_createVarscanObjectFromLine_VarscanHit_v2_2_8(self):
221 line = "C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\n"
222 nbLine = 1
223 launcher = VarscanFile()
224 launcher.setTypeOfVarscanFile("Varscan_2_2_8")
225 obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
226 expVarscanHit = VarscanHit_v2_2_8()
227 expVarscanHit.setChrom('C11HBa0064J13_LR285')
228 expVarscanHit.setPosition('3227')
229 expVarscanHit.setRef('G')
230 expVarscanHit.setVar('A')
231 expVarscanHit.setCns('A')
232 self.assertEquals(expVarscanHit, obsVarscanHit)
233
234 def test_createVarscanObjectFromLine_VarscanHit_v2_2_8_WithTag(self):
235 line = "C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\tEspeceA\n"
236 nbLine = 1
237 launcher = VarscanFile()
238 launcher.setTypeOfVarscanFile("Varscan_2_2_8_WithTag")
239 obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
240 expVarscanHit = VarscanHit_v2_2_8_WithTag()
241 expVarscanHit.setChrom('C11HBa0064J13_LR285')
242 expVarscanHit.setPosition('3227')
243 expVarscanHit.setRef('G')
244 expVarscanHit.setVar('A')
245 expVarscanHit.setCns('A')
246 expVarscanHit.setTag('EspeceA')
247 self.assertEquals(expVarscanHit, obsVarscanHit)
248
249 def _writeVarscanFile(self, varscanFileName):
250 varscanFile = open(varscanFileName, 'w')
251 varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
252 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
253 varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\n")
254 varscanFile.close()
255
256 def _writeVarscanFileWithoutHeader(self, varscanFileName):
257 varscanFile = open(varscanFileName, 'w')
258 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
259 varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\n")
260 varscanFile.close()
261
262 def _writeVarscanFileWithTag(self, varscanFileName):
263 varscanFile = open(varscanFileName, 'w')
264 varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
265 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\tEspeceA\n")
266 varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\tEspeceA\n")
267 varscanFile.close()
268
269 def _writeVarscanFile_v2_2_8(self, varscanFileName):
270 varscanFile = open(varscanFileName, 'w')
271 varscanFile.write("Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\n")
272 varscanFile.write("C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\n")
273 varscanFile.write("C11HBa0064J13_LR285\t3230\tG\tT\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tT\n")
274 varscanFile.close()
275
276 def _writeOther(self, fileName):
277 file = open(fileName, 'w')
278 file.write('##gff-version 3\n')
279 file.write('chr16\tBlatToGff\tBES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n')
280 file.write('chr16\tBlatToGff\tBES\t21736364\t21737069\t.\t+\t.\tID=machin1;Name=machin1;bes_start=21736364;bes_end=21737069;bes_size=22053297\n')
281 file.write('chr11\tBlatToGff\tBES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926\n')
282 file.write('chr11\tBlatToGff\tBES\t3794984\t3795627\t.\t+\t.\tID=machin2;Name=machin2;bes_start=3794984;bes_end=3795627;bes_size=19818926\n')
283 file.write('chr18\tBlatToGff\tBES\t12067347\t12067719\t.\t+\t.\tID=machin3;Name=machin3;bes_start=12067347;bes_end=12067719;bes_size=29360087\n')
284 file.close()
285
286 if __name__ == "__main__":
287 unittest.main()