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1 from commons.core.parsing.VarscanFile import VarscanFile
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2 from commons.core.parsing.VarscanHit import VarscanHit
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3 import unittest
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4 import os
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5 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
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6 from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8
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7 from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag
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8 from commons.core.checker.CheckerException import CheckerException
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9
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10 class Test_VarscanFile(unittest.TestCase):
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11
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12 def test_parse_fileWithHeader(self):
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13 varscanFileName = "file.varscan"
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14 self._writeVarscanFile(varscanFileName)
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15
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16 varscanHit1 = VarscanHit()
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17 varscanHit1.setChrom('C02HBa0291P19_LR48')
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18 varscanHit1.setPosition('32')
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19 varscanHit1.setRef('C')
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20 varscanHit1.setVar('T')
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21
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22 varscanHit2 = VarscanHit()
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23 varscanHit2.setChrom('C02HBa0291P19_LR48')
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24 varscanHit2.setPosition('34')
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25 varscanHit2.setRef('A')
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26 varscanHit2.setVar('T')
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27 expVarscanHitsList = [varscanHit1, varscanHit2]
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28
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29 iVarscanFile = VarscanFile(varscanFileName)
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30 iVarscanFile.parse()
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31 obsVarscanHitsList = iVarscanFile.getVarscanHitsList()
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32 os.remove(varscanFileName)
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33
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34 self.assertEquals(expVarscanHitsList, obsVarscanHitsList)
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35
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36 def test_parse_FileWithoutHeader(self):
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37 varscanFileName = "file.varscan"
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38 self._writeVarscanFileWithoutHeader(varscanFileName)
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39
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40 varscanHit1 = VarscanHit()
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41 varscanHit1.setChrom('C02HBa0291P19_LR48')
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42 varscanHit1.setPosition('32')
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43 varscanHit1.setRef('C')
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44 varscanHit1.setVar('T')
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45
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46 varscanHit2 = VarscanHit()
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47 varscanHit2.setChrom('C02HBa0291P19_LR48')
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48 varscanHit2.setPosition('34')
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49 varscanHit2.setRef('A')
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50 varscanHit2.setVar('T')
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51 expVarscanHitsList = [varscanHit1, varscanHit2]
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52
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53 iVarscanFile = VarscanFile(varscanFileName)
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54 iVarscanFile.parse()
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55 obsVarscanHitsList = iVarscanFile.getVarscanHitsList()
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56 obsTypeOfVarscanFile = iVarscanFile.getTypeOfVarscanFile()
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57 expTypeOfVarscanFile = "Varscan_2_2"
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58
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59 self.assertEquals(expVarscanHitsList, obsVarscanHitsList)
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60 self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile)
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61 os.remove(varscanFileName)
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62
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63 def test_parse_VarscanFileWithTag(self):
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64 inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
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65 self._writeVarscanFileWithTag(inputFileName)
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66 launcher = VarscanFile(inputFileName)
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67 launcher.parse()
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68 obsListOfVarscanHits = launcher.getListOfVarscanHits()
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69
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70 varscanHit1 = VarscanHit_WithTag()
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71 varscanHit1.setChrom('C02HBa0291P19_LR48')
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72 varscanHit1.setPosition('32')
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73 varscanHit1.setRef('C')
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74 varscanHit1.setVar('T')
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75 varscanHit1.setTag('EspeceA')
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76
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77 varscanHit2 = VarscanHit_WithTag()
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78 varscanHit2.setChrom('C02HBa0291P19_LR48')
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79 varscanHit2.setPosition('34')
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80 varscanHit2.setRef('A')
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81 varscanHit2.setVar('T')
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82 varscanHit2.setTag('EspeceA')
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83 expVarscanHitsList = [varscanHit1, varscanHit2]
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84
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85 obsTypeOfVarscanFile = launcher.getTypeOfVarscanFile()
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86 expTypeOfVarscanFile = "Varscan_2_2_WithTag"
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87
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88 self.assertEquals(expVarscanHitsList, obsListOfVarscanHits)
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89 self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile)
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90 os.remove(inputFileName)
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91
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92 def test_parse_VarscanFile_v2_2_8(self):
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93 inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
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94 self._writeVarscanFile_v2_2_8(inputFileName)
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95 launcher = VarscanFile(inputFileName)
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96 launcher.parse()
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97 obsListOfVarscanHits = launcher.getListOfVarscanHits()
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98
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99 varscanHit1 = VarscanHit_v2_2_8()
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100 varscanHit1.setChrom('C11HBa0064J13_LR285')
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101 varscanHit1.setPosition('3227')
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102 varscanHit1.setRef('G')
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103 varscanHit1.setVar('A')
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104 varscanHit1.setCns('A')
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105
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106 varscanHit2 = VarscanHit_v2_2_8()
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107 varscanHit2.setChrom('C11HBa0064J13_LR285')
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108 varscanHit2.setPosition('3230')
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109 varscanHit2.setRef('G')
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110 varscanHit2.setVar('T')
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111 varscanHit2.setCns('T')
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112 expVarscanHitsList = [varscanHit1, varscanHit2]
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113
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114 obsTypeOfVarscanFile = launcher.getTypeOfVarscanFile()
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115 expTypeOfVarscanFile = "Varscan_2_2_8"
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116
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117 self.assertEquals(expVarscanHitsList, obsListOfVarscanHits)
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118 self.assertEquals(expTypeOfVarscanFile, obsTypeOfVarscanFile)
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119 os.remove(inputFileName)
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120
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121 def test_parse_other(self):
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122 inputFileName = "%s/commons/core/parsing/test/varscan.tab" % os.environ["REPET_PATH"]
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123 self._writeOther(inputFileName)
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124 launcher = VarscanFile(inputFileName)
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125 try:
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126 launcher.parse()
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127 except CheckerException, e:
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128 checkerExceptionInstance = e
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129 expMessage = "Warning: this line (l.1) is not a valid varscan line !"
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130 obsMessage = checkerExceptionInstance.msg
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131 os.remove(inputFileName)
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132 self.assertEquals(expMessage, obsMessage)
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133
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134 def test__eq__notEqual(self):
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135 lVarscanHits1 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
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136 iVarscanFile1 = VarscanFile()
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137 iVarscanFile1.setVarscanHitsList(lVarscanHits1)
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138 lVarscanHits2 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "C")]
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139 iVarscanFile2 = VarscanFile()
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140 iVarscanFile2.setVarscanHitsList(lVarscanHits2)
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141
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142 self.assertNotEquals(iVarscanFile1, iVarscanFile2)
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143
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144 def test__eq__equal(self):
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145 lVarscanHits1 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
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146 iVarscanFile1 = VarscanFile()
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147 iVarscanFile1.setVarscanHitsList(lVarscanHits1)
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148 lVarscanHits2 = [VarscanHit("chrom", "12", "T", "G"), VarscanHit("chrom", "14", "T", "G")]
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149 iVarscanFile2 = VarscanFile()
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150 iVarscanFile2.setVarscanHitsList(lVarscanHits2)
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151
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152 self.assertEquals(iVarscanFile1, iVarscanFile2)
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153
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154 def test_selectTypeOfVarscanHitObject_noVarscanHit(self):
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155 launcher = VarscanFile()
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156 launcher.setTypeOfVarscanFile("")
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157 try:
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158 launcher.selectTypeOfVarscanHitObject()
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159 except CheckerException, e:
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160 checkerExceptionInstance = e
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161 expMessage = "Error: no varscan object found !"
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162 obsMessage = checkerExceptionInstance.msg
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163 self.assertEquals(expMessage, obsMessage)
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164
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165 def test_selectTypeOfVarscanHitObject_VarscanHit(self):
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166 launcher = VarscanFile()
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167 launcher.setTypeOfVarscanFile("Varscan_2_2")
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168 obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
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169 expVarscanHit = VarscanHit()
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170 self.assertEquals(expVarscanHit, obsVarscanHit)
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171
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172 def test_selectTypeOfVarscanHitObject_VarscanHitWithTag(self):
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173 launcher = VarscanFile()
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174 launcher.setTypeOfVarscanFile("Varscan_2_2_WithTag")
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175 obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
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176 expVarscanHit = VarscanHit_WithTag()
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177 self.assertEquals(expVarscanHit, obsVarscanHit)
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178
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179 def test_selectTypeOfVarscanHitObject_noVarscanHit_2_2_8(self):
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180 launcher = VarscanFile()
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181 launcher.setTypeOfVarscanFile("Varscan_2_2_8")
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182 obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
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183 expVarscanHit = VarscanHit_v2_2_8()
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184 self.assertEquals(expVarscanHit, obsVarscanHit)
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185
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186 def test_selectTypeOfVarscanHitObject_noVarscanHit_2_2_8_WithTag(self):
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187 launcher = VarscanFile()
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188 launcher.setTypeOfVarscanFile("Varscan_2_2_8_WithTag")
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189 obsVarscanHit = launcher.selectTypeOfVarscanHitObject()
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190 expVarscanHit = VarscanHit_v2_2_8_WithTag()
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191 self.assertEquals(expVarscanHit, obsVarscanHit)
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192
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193 def test_createVarscanObjectFromLine_VarscanHit(self):
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194 line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n"
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195 nbLine = 1
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196 launcher = VarscanFile()
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197 launcher.setTypeOfVarscanFile("Varscan_2_2")
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198 obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
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199 expVarscanHit = VarscanHit()
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200 expVarscanHit.setChrom('C02HBa0291P19_LR48')
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201 expVarscanHit.setPosition('32')
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202 expVarscanHit.setRef('C')
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203 expVarscanHit.setVar('T')
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204 self.assertEquals(expVarscanHit, obsVarscanHit)
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205
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206 def test_createVarscanObjectFromLine_VarscanHitWithTag(self):
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207 line = "C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\tEspeceA\n"
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208 nbLine = 1
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209 launcher = VarscanFile()
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210 launcher.setTypeOfVarscanFile("Varscan_2_2_WithTag")
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211 obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
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212 expVarscanHit = VarscanHit_WithTag()
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213 expVarscanHit.setChrom('C02HBa0291P19_LR48')
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214 expVarscanHit.setPosition('32')
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215 expVarscanHit.setRef('C')
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216 expVarscanHit.setVar('T')
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217 expVarscanHit.setTag('EspeceA')
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218 self.assertEquals(expVarscanHit, obsVarscanHit)
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219
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220 def test_createVarscanObjectFromLine_VarscanHit_v2_2_8(self):
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221 line = "C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\n"
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222 nbLine = 1
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223 launcher = VarscanFile()
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224 launcher.setTypeOfVarscanFile("Varscan_2_2_8")
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225 obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
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226 expVarscanHit = VarscanHit_v2_2_8()
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227 expVarscanHit.setChrom('C11HBa0064J13_LR285')
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228 expVarscanHit.setPosition('3227')
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229 expVarscanHit.setRef('G')
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230 expVarscanHit.setVar('A')
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231 expVarscanHit.setCns('A')
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232 self.assertEquals(expVarscanHit, obsVarscanHit)
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233
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234 def test_createVarscanObjectFromLine_VarscanHit_v2_2_8_WithTag(self):
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235 line = "C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\tEspeceA\n"
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236 nbLine = 1
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237 launcher = VarscanFile()
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238 launcher.setTypeOfVarscanFile("Varscan_2_2_8_WithTag")
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239 obsVarscanHit = launcher.createVarscanObjectFromLine(line, nbLine)
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240 expVarscanHit = VarscanHit_v2_2_8_WithTag()
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241 expVarscanHit.setChrom('C11HBa0064J13_LR285')
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242 expVarscanHit.setPosition('3227')
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243 expVarscanHit.setRef('G')
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244 expVarscanHit.setVar('A')
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245 expVarscanHit.setCns('A')
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246 expVarscanHit.setTag('EspeceA')
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247 self.assertEquals(expVarscanHit, obsVarscanHit)
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248
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249 def _writeVarscanFile(self, varscanFileName):
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250 varscanFile = open(varscanFileName, 'w')
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251 varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
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252 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
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253 varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\n")
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254 varscanFile.close()
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255
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256 def _writeVarscanFileWithoutHeader(self, varscanFileName):
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257 varscanFile = open(varscanFileName, 'w')
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258 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\n")
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259 varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\n")
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260 varscanFile.close()
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261
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262 def _writeVarscanFileWithTag(self, varscanFileName):
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263 varscanFile = open(varscanFileName, 'w')
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264 varscanFile.write("Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n")
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265 varscanFile.write("C02HBa0291P19_LR48\t32\tC\tT\t1\t2\t66,67%\t1\t1\t37\t35\t0.3999999999999999\tEspeceA\n")
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266 varscanFile.write("C02HBa0291P19_LR48\t34\tA\tT\t1\t2\t66,67%\t1\t1\t40\t34\t0.3999999999999999\tEspeceA\n")
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267 varscanFile.close()
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268
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269 def _writeVarscanFile_v2_2_8(self, varscanFileName):
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270 varscanFile = open(varscanFileName, 'w')
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271 varscanFile.write("Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\n")
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272 varscanFile.write("C11HBa0064J13_LR285\t3227\tG\tA\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tA\n")
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273 varscanFile.write("C11HBa0064J13_LR285\t3230\tG\tT\t0\t1\t100%\t0\t1\t0\t54\t0.98\t0\t1\t0\t0\t1\t0\tT\n")
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274 varscanFile.close()
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275
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276 def _writeOther(self, fileName):
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277 file = open(fileName, 'w')
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278 file.write('##gff-version 3\n')
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279 file.write('chr16\tBlatToGff\tBES\t21686950\t21687294\t.\t+\t.\tID=MRRE1H001H13FM1;Name=MRRE1H001H13FM1;bes_start=21686950;bes_end=21687294;bes_size=22053297\n')
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280 file.write('chr16\tBlatToGff\tBES\t21736364\t21737069\t.\t+\t.\tID=machin1;Name=machin1;bes_start=21736364;bes_end=21737069;bes_size=22053297\n')
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281 file.write('chr11\tBlatToGff\tBES\t3725876\t3726473\t.\t+\t.\tID=MRRE1H032F08FM1;Name=MRRE1H032F08FM1;bes_start=3725876;bes_end=3726473;bes_size=19818926\n')
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282 file.write('chr11\tBlatToGff\tBES\t3794984\t3795627\t.\t+\t.\tID=machin2;Name=machin2;bes_start=3794984;bes_end=3795627;bes_size=19818926\n')
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283 file.write('chr18\tBlatToGff\tBES\t12067347\t12067719\t.\t+\t.\tID=machin3;Name=machin3;bes_start=12067347;bes_end=12067719;bes_size=29360087\n')
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284 file.close()
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285
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286 if __name__ == "__main__":
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287 unittest.main() |