Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/test/Test_SsrParser.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 from commons.core.parsing.SsrParser import SsrParser | |
2 import unittest | |
3 | |
4 | |
5 class Test_SsrParser(unittest.TestCase): | |
6 | |
7 | |
8 def test_setAttributesFromString(self): | |
9 ssrLine = "MRRE1H001B07RM1\t1\t2\tta\t19\t153\t190\t734" | |
10 | |
11 iSsrParser = SsrParser() | |
12 iSsrParser.setAttributesFromString(ssrLine) | |
13 | |
14 obsBES_name = iSsrParser.getBesName() | |
15 obsBES_redundancy = iSsrParser.getBesRedundancy() | |
16 obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides() | |
17 obsSSR_Motif = iSsrParser.getSsrMotif() | |
18 obsSSR_Motif_number = iSsrParser.getSsrMotifNumber() | |
19 obsSSR_start = iSsrParser.getSsrStart() | |
20 obsSSR_end = iSsrParser.getSsrEnd() | |
21 obsBES_size = iSsrParser.getBesSize() | |
22 | |
23 expBES_name = 'MRRE1H001B07RM1' | |
24 expBES_redundancy = '1' | |
25 expSSR_nbNucleotides = '2' | |
26 expSSR_Motif = 'ta' | |
27 expSSR_Motif_number = '19' | |
28 expSSR_start = '153' | |
29 expSSR_end = '190' | |
30 expBES_size = '734' | |
31 | |
32 self.assertEquals(expBES_name, obsBES_name) | |
33 self.assertEquals(expBES_redundancy, obsBES_redundancy) | |
34 self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides) | |
35 self.assertEquals(expSSR_Motif, obsSSR_Motif) | |
36 self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number) | |
37 self.assertEquals(expSSR_start, obsSSR_start) | |
38 self.assertEquals(expSSR_end, obsSSR_end) | |
39 self.assertEquals(expBES_size, obsBES_size) | |
40 | |
41 def test_setAttributesFromString_empty_BESName(self): | |
42 ssrLine = "\t1\t2\tta\t19\t153\t190\t734" | |
43 | |
44 iSsrParser = SsrParser() | |
45 iSsrParser.setAttributesFromString(ssrLine) | |
46 | |
47 obsBES_name = iSsrParser.getBesName() | |
48 obsBES_redundancy = iSsrParser.getBesRedundancy() | |
49 obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides() | |
50 obsSSR_Motif = iSsrParser.getSsrMotif() | |
51 obsSSR_Motif_number = iSsrParser.getSsrMotifNumber() | |
52 obsSSR_start = iSsrParser.getSsrStart() | |
53 obsSSR_end = iSsrParser.getSsrEnd() | |
54 obsBES_size = iSsrParser.getBesSize() | |
55 | |
56 expBES_name = '' | |
57 expBES_redundancy = '' | |
58 expSSR_nbNucleotides = '' | |
59 expSSR_Motif = '' | |
60 expSSR_Motif_number = '' | |
61 expSSR_start = '' | |
62 expSSR_end = '' | |
63 expBES_size = '' | |
64 | |
65 self.assertEquals(expBES_name, obsBES_name) | |
66 self.assertEquals(expBES_redundancy, obsBES_redundancy) | |
67 self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides) | |
68 self.assertEquals(expSSR_Motif, obsSSR_Motif) | |
69 self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number) | |
70 self.assertEquals(expSSR_start, obsSSR_start) | |
71 self.assertEquals(expSSR_end, obsSSR_end) | |
72 self.assertEquals(expBES_size, obsBES_size) | |
73 | |
74 def test_setAttributesFromString_less_than_8_fields(self): | |
75 ssrLine = "1\t2\tta\t19\t153\t190\t734" | |
76 | |
77 iSsrParser = SsrParser() | |
78 iSsrParser.setAttributesFromString(ssrLine) | |
79 | |
80 obsBES_name = iSsrParser.getBesName() | |
81 obsBES_redundancy = iSsrParser.getBesRedundancy() | |
82 obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides() | |
83 obsSSR_Motif = iSsrParser.getSsrMotif() | |
84 obsSSR_Motif_number = iSsrParser.getSsrMotifNumber() | |
85 obsSSR_start = iSsrParser.getSsrStart() | |
86 obsSSR_end = iSsrParser.getSsrEnd() | |
87 obsBES_size = iSsrParser.getBesSize() | |
88 | |
89 expBES_name = '' | |
90 expBES_redundancy = '' | |
91 expSSR_nbNucleotides = '' | |
92 expSSR_Motif = '' | |
93 expSSR_Motif_number = '' | |
94 expSSR_start = '' | |
95 expSSR_end = '' | |
96 expBES_size = '' | |
97 | |
98 self.assertEquals(expBES_name, obsBES_name) | |
99 self.assertEquals(expBES_redundancy, obsBES_redundancy) | |
100 self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides) | |
101 self.assertEquals(expSSR_Motif, obsSSR_Motif) | |
102 self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number) | |
103 self.assertEquals(expSSR_start, obsSSR_start) | |
104 self.assertEquals(expSSR_end, obsSSR_end) | |
105 self.assertEquals(expBES_size, obsBES_size) | |
106 | |
107 def test_setAttributes(self): | |
108 lResults = ['MRRE1H001B07RM1','1','2','ta','19','153','190','734'] | |
109 lineNumber = 1 | |
110 | |
111 iSsrParser = SsrParser() | |
112 iSsrParser.setAttributes(lResults, lineNumber) | |
113 | |
114 obsBES_name = iSsrParser.getBesName() | |
115 obsBES_redundancy = iSsrParser.getBesRedundancy() | |
116 obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides() | |
117 obsSSR_Motif = iSsrParser.getSsrMotif() | |
118 obsSSR_Motif_number = iSsrParser.getSsrMotifNumber() | |
119 obsSSR_start = iSsrParser.getSsrStart() | |
120 obsSSR_end = iSsrParser.getSsrEnd() | |
121 obsBES_size = iSsrParser.getBesSize() | |
122 | |
123 expBES_name = 'MRRE1H001B07RM1' | |
124 expBES_redundancy = '1' | |
125 expSSR_nbNucleotides = '2' | |
126 expSSR_Motif = 'ta' | |
127 expSSR_Motif_number = '19' | |
128 expSSR_start = '153' | |
129 expSSR_end = '190' | |
130 expBES_size = '734' | |
131 | |
132 self.assertEquals(expBES_name, obsBES_name) | |
133 self.assertEquals(expBES_redundancy, obsBES_redundancy) | |
134 self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides) | |
135 self.assertEquals(expSSR_Motif, obsSSR_Motif) | |
136 self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number) | |
137 self.assertEquals(expSSR_start, obsSSR_start) | |
138 self.assertEquals(expSSR_end, obsSSR_end) | |
139 self.assertEquals(expBES_size, obsBES_size) | |
140 | |
141 def test_eq_Equals(self): | |
142 SsrParser1 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724') | |
143 SsrParser2 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724') | |
144 | |
145 self.assertTrue(SsrParser1 == SsrParser2) | |
146 | |
147 def test_eq_NotEquals(self): | |
148 SsrParser1 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724') | |
149 SsrParser2 = SsrParser('MRRE1H001A12RM3', '1', '5', 'ttta', '6', '272', '295', '852') | |
150 | |
151 self.assertFalse(SsrParser1 == SsrParser2) | |
152 | |
153 if __name__ == "__main__": | |
154 unittest.main() |