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