Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/test/Test_VarscanHit_WithTag.py @ 6:769e306b7933
Change the repository level.
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.checker.CheckerException import CheckerException | |
3 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag | |
4 | |
5 class Test_VarscanHit_WithTag(unittest.TestCase): | |
6 | |
7 def test_setAttributesFromString(self): | |
8 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\tEspeceA\n" | |
9 | |
10 expChrom = "chr1" | |
11 expPosition = "1804" | |
12 expRef = "T" | |
13 expVar = "C" | |
14 expReadsRef = "0" | |
15 expReadsVar = "1" | |
16 expVarFreq = "100%" | |
17 expStrandsRef = "0" | |
18 expStrandsVar = "1" | |
19 expQualRef = "0" | |
20 expQualVar = "53" | |
21 expPValue = "0.98" | |
22 expTag = "EspeceA" | |
23 | |
24 varscanHit = VarscanHit_WithTag() | |
25 varscanHit.setAttributesFromString(line) | |
26 | |
27 obsChrom = varscanHit.getChrom() | |
28 obsPosition = varscanHit.getPosition() | |
29 obsRef = varscanHit.getRef() | |
30 obsVar = varscanHit.getVar() | |
31 obsReadsRef = varscanHit.getReadsRef() | |
32 obsReadsVar = varscanHit.getReadsVar() | |
33 obsVarFreq = varscanHit.getVarFreq() | |
34 obsStrandsRef = varscanHit.getStrandsRef() | |
35 obsStrandsVar = varscanHit.getStrandsVar() | |
36 obsQualRef = varscanHit.getQualRef() | |
37 obsQualVar = varscanHit.getQualVar() | |
38 obsPValue = varscanHit.getPValue() | |
39 obsTag = varscanHit.getTag() | |
40 | |
41 self.assertEquals(expChrom, obsChrom) | |
42 self.assertEquals(expPosition, obsPosition) | |
43 self.assertEquals(expRef, obsRef) | |
44 self.assertEquals(expVar, obsVar) | |
45 self.assertEquals(expReadsRef, obsReadsRef) | |
46 self.assertEquals(expReadsVar, obsReadsVar) | |
47 self.assertEquals(expVarFreq, obsVarFreq) | |
48 self.assertEquals(expStrandsRef, obsStrandsRef) | |
49 self.assertEquals(expStrandsVar, obsStrandsVar) | |
50 self.assertEquals(expQualRef, obsQualRef) | |
51 self.assertEquals(expQualVar, obsQualVar) | |
52 self.assertEquals(expPValue, obsPValue) | |
53 self.assertEquals(expTag, obsTag) | |
54 | |
55 def test_setAttributesFromString_empty_chrom(self): | |
56 line = "\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\tEspeceA\n" | |
57 varscanHit = VarscanHit_WithTag() | |
58 try : | |
59 varscanHit.setAttributesFromString(line) | |
60 except CheckerException, e: | |
61 checkerExceptionInstance = e | |
62 expMessage = "The field Chrom is empty in varscan file in line " | |
63 obsMessage = checkerExceptionInstance.msg | |
64 self.assertEquals(expMessage, obsMessage) | |
65 | |
66 def test_setAttributes(self): | |
67 lResults = ['chr1', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA'] | |
68 lineNumber = 1 | |
69 | |
70 expChrom = "chr1" | |
71 expPosition = "1804" | |
72 expRef = "T" | |
73 expVar = "C" | |
74 expReadsRef = "0" | |
75 expReadsVar = "1" | |
76 expVarFreq = "100%" | |
77 expStrandsRef = "0" | |
78 expStrandsVar = "1" | |
79 expQualRef = "0" | |
80 expQualVar = "53" | |
81 expPValue = "0.98" | |
82 expTag = "EspeceA" | |
83 | |
84 varscanHit = VarscanHit_WithTag() | |
85 varscanHit.setAttributes(lResults, lineNumber) | |
86 | |
87 obsChrom = varscanHit.getChrom() | |
88 obsPosition = varscanHit.getPosition() | |
89 obsRef = varscanHit.getRef() | |
90 obsVar = varscanHit.getVar() | |
91 obsReadsRef = varscanHit.getReadsRef() | |
92 obsReadsVar = varscanHit.getReadsVar() | |
93 obsVarFreq = varscanHit.getVarFreq() | |
94 obsStrandsRef = varscanHit.getStrandsRef() | |
95 obsStrandsVar = varscanHit.getStrandsVar() | |
96 obsQualRef = varscanHit.getQualRef() | |
97 obsQualVar = varscanHit.getQualVar() | |
98 obsPValue = varscanHit.getPValue() | |
99 obsTag = varscanHit.getTag() | |
100 | |
101 self.assertEquals(expChrom, obsChrom) | |
102 self.assertEquals(expPosition, obsPosition) | |
103 self.assertEquals(expRef, obsRef) | |
104 self.assertEquals(expVar, obsVar) | |
105 self.assertEquals(expReadsRef, obsReadsRef) | |
106 self.assertEquals(expReadsVar, obsReadsVar) | |
107 self.assertEquals(expVarFreq, obsVarFreq) | |
108 self.assertEquals(expStrandsRef, obsStrandsRef) | |
109 self.assertEquals(expStrandsVar, obsStrandsVar) | |
110 self.assertEquals(expQualRef, obsQualRef) | |
111 self.assertEquals(expQualVar, obsQualVar) | |
112 self.assertEquals(expPValue, obsPValue) | |
113 self.assertEquals(expTag, obsTag) | |
114 | |
115 def test_setAttributes_empty_chrom(self): | |
116 lResults = ['', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA'] | |
117 lineNumber = 1 | |
118 | |
119 varscanHit = VarscanHit_WithTag() | |
120 checkerExceptionInstance = None | |
121 try: | |
122 varscanHit.setAttributes(lResults, lineNumber) | |
123 except CheckerException, e: | |
124 checkerExceptionInstance = e | |
125 | |
126 expMessage = "The field Chrom is empty in varscan file in line 1" | |
127 obsMessage = checkerExceptionInstance.msg | |
128 | |
129 self.assertEquals(expMessage, obsMessage) | |
130 | |
131 def test_setAttributes_empty_position(self): | |
132 lResults = ['chr1', '', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA'] | |
133 lineNumber = 1 | |
134 | |
135 varscanHit = VarscanHit_WithTag() | |
136 checkerExceptionInstance = None | |
137 try: | |
138 varscanHit.setAttributes(lResults, lineNumber) | |
139 except CheckerException, e: | |
140 checkerExceptionInstance = e | |
141 | |
142 expMessage = "The field Position is empty in varscan file in line 1" | |
143 obsMessage = checkerExceptionInstance.msg | |
144 | |
145 self.assertEquals(expMessage, obsMessage) | |
146 | |
147 def test_setAttributes_empty_ref(self): | |
148 lResults = ['chr1', '1000', '', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA'] | |
149 lineNumber = 1 | |
150 | |
151 varscanHit = VarscanHit_WithTag() | |
152 checkerExceptionInstance = None | |
153 try: | |
154 varscanHit.setAttributes(lResults, lineNumber) | |
155 except CheckerException, e: | |
156 checkerExceptionInstance = e | |
157 | |
158 expMessage = "The field Ref is empty in varscan file in line 1" | |
159 obsMessage = checkerExceptionInstance.msg | |
160 | |
161 self.assertEquals(expMessage, obsMessage) | |
162 | |
163 def test_setAttributes_empty_cns(self): | |
164 lResults = ['chr1', '1000', 'T', '', '0', '1', '100%', '0', '1', '0', '53', '0.98', 'EspeceA'] | |
165 lineNumber = 1 | |
166 | |
167 varscanHit = VarscanHit_WithTag() | |
168 checkerExceptionInstance = None | |
169 try: | |
170 varscanHit.setAttributes(lResults, lineNumber) | |
171 except CheckerException, e: | |
172 checkerExceptionInstance = e | |
173 | |
174 expMessage = "The field Var is empty in varscan file in line 1" | |
175 obsMessage = checkerExceptionInstance.msg | |
176 | |
177 self.assertEquals(expMessage, obsMessage) | |
178 | |
179 def test__eq__notEquals(self): | |
180 varscanHit1 = VarscanHit_WithTag() | |
181 varscanHit1.setChrom('C02HBa0291P19_LR48') | |
182 varscanHit1.setPosition('34') | |
183 varscanHit1.setRef('A') | |
184 varscanHit1.setVar('T') | |
185 varscanHit1.setVar('EspeceA') | |
186 | |
187 varscanHit2 = VarscanHit_WithTag() | |
188 varscanHit2.setChrom('C02HBa0291P19_LR48') | |
189 varscanHit2.setPosition('34') | |
190 varscanHit2.setRef('A') | |
191 varscanHit2.setVar('T') | |
192 varscanHit2.setVar('EspeceB') | |
193 | |
194 self.assertFalse(varscanHit1 == varscanHit2) | |
195 | |
196 def test__eq__Equals(self): | |
197 varscanHit1 = VarscanHit_WithTag() | |
198 varscanHit1.setChrom('C02HBa0291P19_LR48') | |
199 varscanHit1.setPosition('34') | |
200 varscanHit1.setRef('A') | |
201 varscanHit1.setVar('T') | |
202 varscanHit1.setVar('EspeceA') | |
203 | |
204 varscanHit2 = VarscanHit_WithTag() | |
205 varscanHit2.setChrom('C02HBa0291P19_LR48') | |
206 varscanHit2.setPosition('34') | |
207 varscanHit2.setRef('A') | |
208 varscanHit2.setVar('T') | |
209 varscanHit2.setVar('EspeceA') | |
210 | |
211 if __name__ == "__main__": | |
212 unittest.main() |