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6
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1 import unittest
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2 from commons.core.checker.CheckerException import CheckerException
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3 from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8
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4 from commons.core.parsing.VarscanHit import VarscanHit
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5
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6 class Test_VarscanHit_v2_2_8(unittest.TestCase):
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7
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8 def test_setAttributesFromString(self):
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9 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\n"
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10
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11 expChrom = "chr1"
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12 expPosition = "1804"
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13 expRef = "T"
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14 expCns = "C"
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15 expReadsRef = "0"
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16 expReadsVar = "1"
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17 expVarFreq = "100%"
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18 expStrandsRef = "0"
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19 expStrandsVar = "1"
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20 expQualRef = "0"
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21 expQualVar = "53"
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22 expPValue = "0.98"
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23 expMapQualRef = "0"
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24 expMapQualVar = "1"
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25 expReadsRefPlus = "0"
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26 expReadsRefMinus = "0"
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27 expReadsVarPlus = "1"
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28 expReadsVarMinus = "0"
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29 expVar = "C"
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30
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31 varscanHit = VarscanHit_v2_2_8()
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32 varscanHit.setAttributesFromString(line)
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33
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34 obsChrom = varscanHit.getChrom()
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35 obsPosition = varscanHit.getPosition()
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36 obsRef = varscanHit.getRef()
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37 obsCns = varscanHit.getCns()
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38 obsReadsRef = varscanHit.getReadsRef()
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39 obsReadsVar = varscanHit.getReadsVar()
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40 obsVarFreq = varscanHit.getVarFreq()
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41 obsStrandsRef = varscanHit.getStrandsRef()
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42 obsStrandsVar = varscanHit.getStrandsVar()
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43 obsQualRef = varscanHit.getQualRef()
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44 obsQualVar = varscanHit.getQualVar()
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45 obsPValue = varscanHit.getPValue()
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46 obsMapQualRef = varscanHit.getMapQualRef()
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47 obsMapQualVar = varscanHit.getMapQualVar()
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48 obsReadsRefPlus = varscanHit.getReadsRefPlus()
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49 obsReadsRefMinus = varscanHit.getReadsRefMinus()
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50 obsReadsVarPlus = varscanHit.getReadsVarPlus()
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51 obsReadsVarMinus = varscanHit.getReadsVarMinus()
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52 obsVar = varscanHit.getVar()
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53
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54 self.assertEquals(expChrom, obsChrom)
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55 self.assertEquals(expPosition, obsPosition)
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56 self.assertEquals(expRef, obsRef)
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57 self.assertEquals(expCns, obsCns)
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58 self.assertEquals(expReadsRef, obsReadsRef)
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59 self.assertEquals(expReadsVar, obsReadsVar)
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60 self.assertEquals(expVarFreq, obsVarFreq)
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61 self.assertEquals(expStrandsRef, obsStrandsRef)
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62 self.assertEquals(expStrandsVar, obsStrandsVar)
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63 self.assertEquals(expQualRef, obsQualRef)
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64 self.assertEquals(expQualVar, obsQualVar)
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65 self.assertEquals(expPValue, obsPValue)
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66 self.assertEquals(expMapQualRef, obsMapQualRef)
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67 self.assertEquals(expMapQualVar, obsMapQualVar)
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68 self.assertEquals(expReadsRefPlus, obsReadsRefPlus)
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69 self.assertEquals(expReadsRefMinus, obsReadsRefMinus)
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70 self.assertEquals(expReadsVarPlus, obsReadsVarPlus)
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71 self.assertEquals(expReadsVarMinus, obsReadsVarMinus)
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72 self.assertEquals(expVar, obsVar)
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73
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74 def test_setAttributesFromString_empty_chrom(self):
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75 line = "\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\n"
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76 varscanHit = VarscanHit_v2_2_8()
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77 try :
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78 varscanHit.setAttributesFromString(line)
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79 except CheckerException, e:
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80 checkerExceptionInstance = e
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81 expMessage = "The field Chrom is empty in varscan file in line "
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82 obsMessage = checkerExceptionInstance.msg
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83 self.assertEquals(expMessage, obsMessage)
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84
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85 def test_setAttributesFromString_less_than_19_fields(self):
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86 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\n"
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87 varscanHit = VarscanHit_v2_2_8()
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88 try :
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89 varscanHit.setAttributesFromString(line)
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90 except CheckerException, e:
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91 checkerExceptionInstance = e
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92 expMessage = "This varscan line (l.) is not complete"
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93 obsMessage = checkerExceptionInstance.msg
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94 self.assertEquals(expMessage, obsMessage)
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95
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96 def test_setAttributes(self):
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97 lResults = ['chr1', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C']
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98 lineNumber = 1
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99
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100 expChrom = "chr1"
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101 expPosition = "1804"
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102 expRef = "T"
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103 expCns = "C"
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104 expReadsRef = "0"
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105 expReadsVar = "1"
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106 expVarFreq = "100%"
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107 expStrandsRef = "0"
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108 expStrandsVar = "1"
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109 expQualRef = "0"
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110 expQualVar = "53"
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111 expPValue = "0.98"
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112 expMapQualRef = "0"
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113 expMapQualVar = "1"
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114 expReadsRefPlus = "0"
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115 expReadsRefMinus = "0"
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116 expReadsVarPlus = "1"
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117 expReadsVarMinus = "0"
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118 expVar = "C"
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119
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120 varscanHit = VarscanHit_v2_2_8()
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121 varscanHit.setAttributes(lResults, lineNumber)
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122
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123 obsChrom = varscanHit.getChrom()
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124 obsPosition = varscanHit.getPosition()
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125 obsRef = varscanHit.getRef()
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126 obsCns = varscanHit.getCns()
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127 obsReadsRef = varscanHit.getReadsRef()
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128 obsReadsVar = varscanHit.getReadsVar()
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129 obsVarFreq = varscanHit.getVarFreq()
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130 obsStrandsRef = varscanHit.getStrandsRef()
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131 obsStrandsVar = varscanHit.getStrandsVar()
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132 obsQualRef = varscanHit.getQualRef()
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133 obsQualVar = varscanHit.getQualVar()
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134 obsPValue = varscanHit.getPValue()
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135 obsMapQualRef = varscanHit.getMapQualRef()
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136 obsMapQualVar = varscanHit.getMapQualVar()
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137 obsReadsRefPlus = varscanHit.getReadsRefPlus()
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138 obsReadsRefMinus = varscanHit.getReadsRefMinus()
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139 obsReadsVarPlus = varscanHit.getReadsVarPlus()
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140 obsReadsVarMinus = varscanHit.getReadsVarMinus()
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141 obsVar = varscanHit.getVar()
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142
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143 self.assertEquals(expChrom, obsChrom)
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144 self.assertEquals(expPosition, obsPosition)
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145 self.assertEquals(expRef, obsRef)
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146 self.assertEquals(expCns, obsCns)
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147 self.assertEquals(expReadsRef, obsReadsRef)
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148 self.assertEquals(expReadsVar, obsReadsVar)
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149 self.assertEquals(expVarFreq, obsVarFreq)
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150 self.assertEquals(expStrandsRef, obsStrandsRef)
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151 self.assertEquals(expStrandsVar, obsStrandsVar)
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152 self.assertEquals(expQualRef, obsQualRef)
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153 self.assertEquals(expQualVar, obsQualVar)
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154 self.assertEquals(expPValue, obsPValue)
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155 self.assertEquals(expMapQualRef, obsMapQualRef)
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156 self.assertEquals(expMapQualVar, obsMapQualVar)
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157 self.assertEquals(expReadsRefPlus, obsReadsRefPlus)
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158 self.assertEquals(expReadsRefMinus, obsReadsRefMinus)
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159 self.assertEquals(expReadsVarPlus, obsReadsVarPlus)
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160 self.assertEquals(expReadsVarMinus, obsReadsVarMinus)
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161 self.assertEquals(expVar, obsVar)
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162
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163 def test_setAttributes_empty_chrom(self):
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164 lResults = ['', '1804', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C']
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165 lineNumber = 1
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166
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167 varscanHit = VarscanHit_v2_2_8()
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168 checkerExceptionInstance = None
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169 try:
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170 varscanHit.setAttributes(lResults, lineNumber)
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171 except CheckerException, e:
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172 checkerExceptionInstance = e
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173
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174 expMessage = "The field Chrom is empty in varscan file in line 1"
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175 obsMessage = checkerExceptionInstance.msg
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176
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177 self.assertEquals(expMessage, obsMessage)
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178
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179 def test_setAttributes_empty_position(self):
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180 lResults = ['chr1', '', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C']
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181 lineNumber = 1
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182
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183 varscanHit = VarscanHit_v2_2_8()
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184 checkerExceptionInstance = None
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185 try:
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186 varscanHit.setAttributes(lResults, lineNumber)
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187 except CheckerException, e:
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188 checkerExceptionInstance = e
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189
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190 expMessage = "The field Position is empty in varscan file in line 1"
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191 obsMessage = checkerExceptionInstance.msg
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192
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193 self.assertEquals(expMessage, obsMessage)
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194
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195 def test_setAttributes_empty_ref(self):
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196 lResults = ['chr1', '1000', '', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C']
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197 lineNumber = 1
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198
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199 varscanHit = VarscanHit_v2_2_8()
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200 checkerExceptionInstance = None
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201 try:
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202 varscanHit.setAttributes(lResults, lineNumber)
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203 except CheckerException, e:
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204 checkerExceptionInstance = e
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205
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206 expMessage = "The field Ref is empty in varscan file in line 1"
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207 obsMessage = checkerExceptionInstance.msg
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208
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209 self.assertEquals(expMessage, obsMessage)
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210
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211 def test_setAttributes_empty_cns(self):
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212 lResults = ['chr1', '1000', 'T', '', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', 'C']
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213 lineNumber = 1
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214
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215 varscanHit = VarscanHit_v2_2_8()
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216 checkerExceptionInstance = None
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217 try:
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218 varscanHit.setAttributes(lResults, lineNumber)
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219 except CheckerException, e:
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220 checkerExceptionInstance = e
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221
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222 expMessage = "The field Cons is empty in varscan file in line 1"
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223 obsMessage = checkerExceptionInstance.msg
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224
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225 self.assertEquals(expMessage, obsMessage)
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226
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227 def test_setAttributes_empty_var(self):
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228 lResults = ['chr1', '1000', 'T', 'C', '0', '1', '100%', '0', '1', '0', '53', '0.98', '0', '1', '0', '0', '1', '0', '']
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229 lineNumber = 1
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230
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231 varscanHit = VarscanHit_v2_2_8()
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232 checkerExceptionInstance = None
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233 try:
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234 varscanHit.setAttributes(lResults, lineNumber)
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235 except CheckerException, e:
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236 checkerExceptionInstance = e
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237
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238 expMessage = "The field varAllele is empty in varscan file in line 1"
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239 obsMessage = checkerExceptionInstance.msg
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240
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241 self.assertEquals(expMessage, obsMessage)
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242
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243 def test__eq__notEquals(self):
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244 varscanHit1 = VarscanHit_v2_2_8()
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245 varscanHit1.setChrom('C02HBa0291P19_LR48')
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246 varscanHit1.setPosition('32')
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247 varscanHit1.setRef('C')
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248 varscanHit1.setCns('T')
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249 varscanHit1.setVar('T')
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250
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251 varscanHit2 = VarscanHit_v2_2_8()
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252 varscanHit2.setChrom('C02HBa0291P19_LR48')
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253 varscanHit2.setPosition('34')
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254 varscanHit2.setRef('A')
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255 varscanHit2.setCns('T')
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256 varscanHit2.setVar('T')
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257
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258 self.assertFalse(varscanHit1 == varscanHit2)
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259
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260 def test__eq__Equals(self):
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261 varscanHit1 = VarscanHit_v2_2_8()
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262 varscanHit1.setChrom('C02HBa0291P19_LR48')
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263 varscanHit1.setPosition('34')
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264 varscanHit1.setRef('A')
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265 varscanHit1.setCns('T')
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266 varscanHit1.setVar('T')
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267
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268 varscanHit2 = VarscanHit_v2_2_8()
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269 varscanHit2.setChrom('C02HBa0291P19_LR48')
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270 varscanHit2.setPosition('34')
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271 varscanHit2.setRef('A')
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272 varscanHit2.setCns('T')
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273 varscanHit2.setVar('T')
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274
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275 self.assertTrue(varscanHit1 == varscanHit2)
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276
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277 def test_convertVarscanHit_v2_2_8_To_VarscanHit(self):
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278 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\t0\t1\t0\t0\t1\t0\tC\n"
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279 iVarscanHit_v2_2_8_WithTag = VarscanHit_v2_2_8()
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280 iVarscanHit_v2_2_8_WithTag.setAttributesFromString(line)
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281 obsVarcanHit_WithTag = iVarscanHit_v2_2_8_WithTag.convertVarscanHit_v2_2_8_To_VarscanHit()
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282
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283 line = "chr1\t1804\tT\tC\t0\t1\t100%\t0\t1\t0\t53\t0.98\n"
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284 expVarcanHit_WithTag = VarscanHit()
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285 expVarcanHit_WithTag.setAttributesFromString(line)
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286
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287 self.assertEquals(expVarcanHit_WithTag, obsVarcanHit_WithTag)
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288
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289 if __name__ == "__main__":
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290 unittest.main() |
