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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.checker.CheckerException import CheckerException
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33 from commons.core.parsing.VarscanHit import VarscanHit
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34
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35 class VarscanHit_v2_2_8(VarscanHit):
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36
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37 def __init__(self, chrom = "", position = "", ref = "", cns = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = "", mapQualRef = "", mapQualVar = "", readsRefPlus = "", readsRefMinus = "", readsVarPlus = "", readsVarMinus = "", var = ""):
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38 self._cns = cns
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39 self._mapQualRef = mapQualRef
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40 self._mapQualVar = mapQualVar
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41 self._readsRefPlus = readsRefPlus
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42 self._readsRefMinus = readsRefMinus
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43 self._readsVarPlus = readsVarPlus
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44 self._readsVarMinus = readsVarMinus
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45 VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue)
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46
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47 ## Equal operator
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48 #
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49 # @param o a VarscanFileAnalysis instance
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50 #
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51 def __eq__(self, o):
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52 if self._cns == o._cns:
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53 return VarscanHit.__eq__(self, o)
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54 return False
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55
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56 def setCns(self, consensus):
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57 self._cns = consensus
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58
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59 def setMapQualRef(self, mapQualRef):
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60 self._mapQualRef = mapQualRef
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61
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62 def setMapQualVar(self, mapQualVar):
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63 self._mapQualVar = mapQualVar
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64
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65 def setReadsRefPlus(self, readsRefPlus):
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66 self._readsRefPlus = readsRefPlus
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67
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68 def setReadsRefMinus(self, readsRefMinus):
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69 self._readsRefMinus = readsRefMinus
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70
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71 def setReadsVarPlus(self, readsVarPlus):
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72 self._readsVarPlus = readsVarPlus
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73
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74 def setReadsVarMinus(self, readsVarMinus):
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75 self._readsVarMinus = readsVarMinus
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76
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77 def getCns(self):
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78 return self._cns
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79
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80 def getMapQualRef(self):
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81 return self._mapQualRef
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82
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83 def getMapQualVar(self):
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84 return self._mapQualVar
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85
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86 def getReadsRefPlus(self):
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87 return self._readsRefPlus
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88
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89 def getReadsRefMinus(self):
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90 return self._readsRefMinus
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91
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92 def getReadsVarPlus(self):
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93 return self._readsVarPlus
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94
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95 def getReadsVarMinus(self):
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96 return self._readsVarMinus
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97
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98 def getHeader(self):
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99 return "Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\n"
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100
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101 def getVarscanLine(self):
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102 return "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (self.getChrom(), self.getPosition(), self.getRef(), self.getCns(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(), self.getQualRef(), self.getQualVar(), self.getPValue(), self.getMapQualRef(), self.getMapQualVar(), self.getReadsRefPlus(), self.getReadsRefMinus(), self.getReadsVarPlus(), self.getReadsVarMinus(), self.getVar())
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103
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104 def setAttributes(self, lResults, iCurrentLineNumber):
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105 if lResults[0] != '':
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106 self.setChrom(lResults[0])
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107 else:
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108 raise CheckerException ("The field Chrom is empty in varscan file in line %s" % iCurrentLineNumber)
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109 if lResults[1] != '':
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110 self.setPosition(lResults[1])
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111 else:
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112 raise CheckerException ("The field Position is empty in varscan file in line %s" % iCurrentLineNumber)
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113 if lResults[2] != '':
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114 self.setRef(lResults[2])
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115 else:
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116 raise CheckerException ("The field Ref is empty in varscan file in line %s" % iCurrentLineNumber)
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117 if lResults[3] != '':
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118 self.setCns(lResults[3])
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119 else:
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120 raise CheckerException ("The field Cons is empty in varscan file in line %s" % iCurrentLineNumber)
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121 if lResults[4] != '':
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122 self.setReadsRef(lResults[4])
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123 if lResults[5] != '':
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124 self.setReadsVar(lResults[5])
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125 if lResults[6] != '':
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126 self.setVarFreq(lResults[6])
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127 if lResults[7] != '':
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128 self.setStrandsRef(lResults[7])
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129 if lResults[8] != '':
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130 self.setStrandsVar(lResults[8])
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131 if lResults[9] != '':
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132 self.setQualRef(lResults[9])
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133 if lResults[10] != '':
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134 self.setQualVar(lResults[10])
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135 if lResults[11] != '':
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136 self.setPValue(lResults[11])
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137 if lResults[12] != '':
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138 self.setMapQualRef(lResults[12])
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139 if lResults[13] != '':
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140 self.setMapQualVar(lResults[13])
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141 if lResults[14] != '':
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142 self.setReadsRefPlus(lResults[14])
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143 if lResults[15] != '':
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144 self.setReadsRefMinus(lResults[15])
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145 if lResults[16] != '':
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146 self.setReadsVarPlus(lResults[16])
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147 if lResults[17] != '':
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148 self.setReadsVarMinus(lResults[17])
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149 if lResults[18] != '':
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150 self.setVar(lResults[18])
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151 else:
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152 raise CheckerException ("The field varAllele is empty in varscan file in line %s" % iCurrentLineNumber)
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153
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154 def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
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155 varscanString = varscanString.rstrip()
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156 lvarscanStringItem = varscanString.split(fieldSeparator)
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157 if len(lvarscanStringItem) < 19:
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158 raise CheckerException ("This varscan line (l.%s) is not complete" % iCurrentLineNumber)
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159 self.setAttributes(lvarscanStringItem, iCurrentLineNumber)
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160
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161 def convertVarscanHit_v2_2_8_To_VarscanHit(self):
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162 iVarscanHit = VarscanHit()
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163 iVarscanHit.setChrom(self.getChrom())
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164 iVarscanHit.setPosition(self.getPosition())
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165 iVarscanHit.setRef(self.getRef())
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166 iVarscanHit.setVar(self.getVar())
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167 iVarscanHit.setReadsRef(self.getReadsRef())
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168 iVarscanHit.setReadsVar(self.getReadsVar())
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169 iVarscanHit.setVarFreq(self.getVarFreq())
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170 iVarscanHit.setStrandsRef(self.getStrandsRef())
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171 iVarscanHit.setStrandsVar(self.getStrandsVar())
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172 iVarscanHit.setQualRef(self.getQualRef())
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173 iVarscanHit.setQualVar(self.getQualVar())
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174 iVarscanHit.setPValue(self.getPValue())
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175 return iVarscanHit
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176 |