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comparison commons/core/parsing/test/Test_SsrParser.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.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()