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6
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1 import unittest
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2 from commons.core.parsing.VarscanHit import VarscanHit
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3 from commons.core.checker.CheckerException import CheckerException
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4
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5 class Test_VarscanHit(unittest.TestCase):
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6
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7 def test_setAttributesFromString(self):
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8 line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n"
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9
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10 expChrom = "C02HBa0291P19_LR48"
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11 expPosition = "32"
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12 expRef = "C"
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13 expVar = "T"
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14
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15 varscanHit = VarscanHit()
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16 varscanHit.setAttributesFromString(line)
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17
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18 obsChrom = varscanHit.getChrom()
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19 obsPosition = varscanHit.getPosition()
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20 obsRef = varscanHit.getRef()
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21 obsVar = varscanHit.getVar()
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22
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23 self.assertEquals(expChrom, obsChrom)
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24 self.assertEquals(expPosition, obsPosition)
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25 self.assertEquals(expRef, obsRef)
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26 self.assertEquals(expVar, obsVar)
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27
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28 def test_setAttributesFromString_empty_chrom(self):
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29 line = "\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n"
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30 iVarscanHit = VarscanHit()
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31 try :
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32 iVarscanHit.setAttributesFromString(line)
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33 except CheckerException, e:
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34 checkerExceptionInstance = e
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35
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36 expMessage = "The field Chrom is empty in varscan file in line "
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37 obsMessage = checkerExceptionInstance.msg
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38
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39 self.assertEquals(expMessage, obsMessage)
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40
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41 def test_setAttributesFromString_less_than_12_fields(self):
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42 line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\n"
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43 iVarscanHit = VarscanHit()
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44 iVarscanHit.setAttributesFromString(line)
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45 self.assertEquals("", iVarscanHit.getQualVar())
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46 self.assertEquals("", iVarscanHit.getPValue())
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47
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48 def test_setAttributes(self):
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49 lResults = ["C02HBa0291P19_LR48", "32", "C", "T", "1", "2", "66,67%", "1", "1", "37", "35", "0.3999999999999999"]
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50 lineNumber = 1
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51
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52 expChrom = "C02HBa0291P19_LR48"
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53 expPosition = "32"
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54 expRef = "C"
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55 expVar = "T"
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56
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57 varscanHit = VarscanHit()
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58 varscanHit.setAttributes(lResults, lineNumber)
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59
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60 obsChrom = varscanHit.getChrom()
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61 obsPosition = varscanHit.getPosition()
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62 obsRef = varscanHit.getRef()
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63 obsVar = varscanHit.getVar()
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64
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65 self.assertEquals(expChrom, obsChrom)
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66 self.assertEquals(expPosition, obsPosition)
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67 self.assertEquals(expRef, obsRef)
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68 self.assertEquals(expVar, obsVar)
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69
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70 def test_setAttributes_empty_chrom(self):
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71 lResults = ["", "", "", "", "", "", "10", "", "", "", "", ""]
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72 lineNumber = 1
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73
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74 varscanHit = VarscanHit()
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75 checkerExceptionInstance = None
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76 try:
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77 varscanHit.setAttributes(lResults, lineNumber)
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78 except CheckerException, e:
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79 checkerExceptionInstance = e
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80
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81 expMessage = "The field Chrom is empty in varscan file in line 1"
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82 obsMessage = checkerExceptionInstance.msg
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83
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84 self.assertEquals(expMessage, obsMessage)
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85
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86 def test_setAttributes_empty_position(self):
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87 lResults = ["chrom", "", "", "", "", "", "10", "", "", "", "", ""]
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88 lineNumber = 5
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89
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90 varscanHit = VarscanHit()
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91 checkerExceptionInstance = None
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92 try:
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93 varscanHit.setAttributes(lResults, lineNumber)
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94 except CheckerException, e:
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95 checkerExceptionInstance = e
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96
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97 expMessage = "The field Position is empty in varscan file in line 5"
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98 obsMessage = checkerExceptionInstance.msg
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99
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100 self.assertEquals(expMessage, obsMessage)
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101
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102 def test_setAttributes_empty_ref(self):
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103 lResults = ["chrom", "position", "", "", "", "", "10", "", "", "", "", ""]
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104 lineNumber = 5
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105
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106 varscanHit = VarscanHit()
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107 checkerExceptionInstance = None
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108 try:
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109 varscanHit.setAttributes(lResults, lineNumber)
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110 except CheckerException, e:
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111 checkerExceptionInstance = e
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112
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113 expMessage = "The field Ref is empty in varscan file in line 5"
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114 obsMessage = checkerExceptionInstance.msg
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115
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116 self.assertEquals(expMessage, obsMessage)
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117
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118 def test_setAttributes_empty_var(self):
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119 lResults = ["chrom", "position", "ref", "", "", "", "10", "", "", "", "", ""]
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120 lineNumber = 5
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121
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122 varscanHit = VarscanHit()
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123 checkerExceptionInstance = None
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124 try:
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125 varscanHit.setAttributes(lResults, lineNumber)
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126 except CheckerException, e:
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127 checkerExceptionInstance = e
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128
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129 expMessage = "The field Var is empty in varscan file in line 5"
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130 obsMessage = checkerExceptionInstance.msg
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131
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132 self.assertEquals(expMessage, obsMessage)
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133
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134 def test__eq__notEquals(self):
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135 varscanHit1 = VarscanHit()
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136 varscanHit1.setChrom('C02HBa0291P19_LR48')
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137 varscanHit1.setPosition('32')
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138 varscanHit1.setRef('C')
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139 varscanHit1.setVar('T')
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140
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141 varscanHit2 = VarscanHit()
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142 varscanHit2.setChrom('C02HBa0291P19_LR48')
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143 varscanHit2.setPosition('34')
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144 varscanHit2.setRef('A')
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145 varscanHit2.setVar('T')
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146
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147 self.assertFalse(varscanHit1 == varscanHit2)
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148
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149 def test__eq__Equals(self):
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150 varscanHit1 = VarscanHit()
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151 varscanHit1.setChrom('C02HBa0291P19_LR48')
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152 varscanHit1.setPosition('32')
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153 varscanHit1.setRef('C')
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154 varscanHit1.setVar('T')
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155
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156 varscanHit2 = VarscanHit()
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157 varscanHit2.setChrom('C02HBa0291P19_LR48')
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158 varscanHit2.setPosition('32')
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159 varscanHit2.setRef('C')
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160 varscanHit2.setVar('T')
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161
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162 self.assertTrue(varscanHit1 == varscanHit2)
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163
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164 if __name__ == "__main__":
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165 unittest.main() |
