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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 from commons.core.parsing.VarscanHit import VarscanHit
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33 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
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34 from commons.core.parsing.VarscanHit_v2_2_8 import VarscanHit_v2_2_8
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35 from commons.core.checker.CheckerException import CheckerException
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36 from commons.core.parsing.VarscanHit_v2_2_8_WithTag import VarscanHit_v2_2_8_WithTag
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37
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38 class VarscanFile(object):
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39
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40 def __init__(self, varscanFileName = ""):
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41 self._varscanFileName = varscanFileName
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42 self._varscanFieldSeparator = "\t"
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43 self._lVarscanHits = []
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44 self._typeOfVarscanFile = ""
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45
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46 def __eq__(self, o):
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47 return self._varscanFieldSeparator == o._varscanFieldSeparator and self._lVarscanHits == o._lVarscanHits and self._varscanFileName == o._varscanFileName
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48
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49 def setVarscanHitsList(self, lVarscanHits):
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50 self._lVarscanHits = lVarscanHits
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51
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52 def setHeaderVarcanFile(self, headerVarcanFile):
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53 self._headerVarcanFile = headerVarcanFile
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54
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55 def setTypeOfVarscanFile(self, type):
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56 if type == "Varscan_2_2" or type == "Varscan_2_2_WithTag" or type == "Varscan_2_2_8" or type == "Varscan_2_2_8_WithTag":
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57 self._typeOfVarscanFile = type
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58 else:
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59 self._typeOfVarscanFile = ""
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60
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61 def getVarscanHitsList(self):
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62 return self._lVarscanHits
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63
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64 def getHeaderVarcanFile(self):
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65 return self._headerVarcanFile
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66
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67 def getListOfVarscanHits(self):
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68 return self._lVarscanHits
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69
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70 def getTypeOfVarscanFile(self):
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71 return self._typeOfVarscanFile
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72
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73 def parse(self):
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74 varscanFile = open(self._varscanFileName, "r")
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75 currentLineNumber = 0
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76 line = varscanFile.readline()
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77 if "Chrom\tPosition" in line:
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78 self.setHeaderVarcanFile(line)
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79 line = varscanFile.readline()
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80 while line != "":
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81 if not "Chrom\tPosition" in line:
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82 currentLineNumber += 1
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83 line = line.strip()
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84 lResults = line.split(self._varscanFieldSeparator)
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85 if len(lResults) == 12:
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86 currentVarscanLine = self.createVarscanHit(line, currentLineNumber)
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87 self._typeOfVarscanFile = "Varscan_2_2"
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88 elif len(lResults) == 13:
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89 currentVarscanLine = self.createVarscanHitWithTag(line, currentLineNumber)
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90 self._typeOfVarscanFile = "Varscan_2_2_WithTag"
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91 elif len(lResults) == 19:
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92 currentVarscanLine = self.createVarscanHit_v2_2_8(line, currentLineNumber)
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93 self._typeOfVarscanFile = "Varscan_2_2_8"
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94 elif len(lResults) == 20:
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95 currentVarscanLine = self.createVarscanHit_v2_2_8_WithTag(line, currentLineNumber)
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96 self._typeOfVarscanFile = "Varscan_2_2_8_WithTag"
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97 else:
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98 raise CheckerException ("Warning: this line (l.%s) is not a valid varscan line !" % currentLineNumber)
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99 self._lVarscanHits.append(currentVarscanLine)
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100 line = varscanFile.readline()
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101 varscanFile.close()
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102
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103 def createVarscanObjectFromLine(self, line, currentLineNumber):
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104 if self._typeOfVarscanFile == "Varscan_2_2":
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105 VarscanHit = self.createVarscanHit(line, currentLineNumber)
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106 return VarscanHit
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107 elif self._typeOfVarscanFile == "Varscan_2_2_WithTag":
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108 return self.createVarscanHitWithTag(line, currentLineNumber)
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109 elif self._typeOfVarscanFile == "Varscan_2_2_8":
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110 return self.createVarscanHit_v2_2_8(line, currentLineNumber)
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111 elif self._typeOfVarscanFile == "Varscan_2_2_8_WithTag":
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112 return self.createVarscanHit_v2_2_8_WithTag(line, currentLineNumber)
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113
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114 def createVarscanHit(self, line, currentLineNumber):
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115 iVarscanHit = VarscanHit()
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116 iVarscanHit.setAttributesFromString(line, currentLineNumber)
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117 return iVarscanHit
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118
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119 def createVarscanHitWithTag(self, line, currentLineNumber):
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120 iVarscanHitWithTag = VarscanHit_WithTag()
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121 iVarscanHitWithTag.setAttributesFromString(line, currentLineNumber)
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122 return iVarscanHitWithTag
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123
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124 def createVarscanHit_v2_2_8(self, line, currentLineNumber):
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125 iVarscanHit = VarscanHit_v2_2_8()
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126 iVarscanHit.setAttributesFromString(line, currentLineNumber)
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127 return iVarscanHit
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128
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129 def createVarscanHit_v2_2_8_WithTag(self, line, currentLineNumber):
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130 iVarscanHitWithTag = VarscanHit_v2_2_8_WithTag()
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131 iVarscanHitWithTag.setAttributesFromString(line, currentLineNumber)
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132 return iVarscanHitWithTag
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133
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134 def selectTypeOfVarscanHitObject(self):
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135 if self._typeOfVarscanFile == "":
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136 raise CheckerException ("Error: no varscan object found !")
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137 elif self._typeOfVarscanFile == "Varscan_2_2":
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138 return VarscanHit()
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139 elif self._typeOfVarscanFile == "Varscan_2_2_WithTag":
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140 return VarscanHit_WithTag()
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141 elif self._typeOfVarscanFile == "Varscan_2_2_8":
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142 return VarscanHit_v2_2_8()
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143 elif self._typeOfVarscanFile == "Varscan_2_2_8_WithTag":
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144 return VarscanHit_v2_2_8_WithTag()
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145 |
