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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 import re
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35
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36 class VarscanHitForGnpSNP(VarscanHit):
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37
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38 def __init__(self):
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39 VarscanHit.__init__(self)
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40 self._reads1 = ''
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41 self._reads2 = ''
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42 self._varFreq = ''
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43 self._strands1 = ''
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44 self._strands2 = ''
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45 self._qual1 = ''
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46 self._qual2 = ''
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47 self._pvalue = ''
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48 self._5flank = ''
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49 self._3flank = ''
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50 self._gnpSnp_ref = ''
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51 self._gnpSnp_var = ''
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52 self._gnpSnp_position = 0
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53 self._polymType = ''
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54 self._polymLength = 0
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55 self._occurrence = 1
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56
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57 ## Equal operator
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58 #
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59 # @param o a VarscanFileAnalysis instance
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60 #
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61 def __eq__(self, o):
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62 return VarscanHit.__eq__(self, o) \
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63 and self._reads1 == o._reads1 and self._reads2 == o._reads2 \
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64 and self._varFreq == o._varFreq and self._strands1 == o._strands1 \
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65 and self._strands2 == o._strands2 and self._qual1 == o._qual1 \
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66 and self._qual2 == o._qual2 and self._pvalue == o._pvalue \
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67 and self._3flank == o._3flank and self._5flank == o._5flank \
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68 and self._gnpSnp_position == o._gnpSnp_position and self._gnpSnp_ref == o._gnpSnp_ref \
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69 and self._gnpSnp_var == o._gnpSnp_var and self._polymLength == o._polymLength \
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70 and self._polymType == o._polymType and self._occurrence == o._occurrence
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71
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72 def isPolymTypeAlreadyFoundAtThisChromAndThisPosition(self, iVarscanHitForGnpSNP):
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73 return self._chrom == iVarscanHitForGnpSNP.getChrom() \
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74 and self._position == iVarscanHitForGnpSNP.getPosition() \
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75 and self._polymType == iVarscanHitForGnpSNP.getPolymType()
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76
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77 def manageOccurrence(self, iVarscanHitForGnpSNP=None):
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78 if iVarscanHitForGnpSNP != None and self.isPolymTypeAlreadyFoundAtThisChromAndThisPosition(iVarscanHitForGnpSNP):
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79 self._occurrence = iVarscanHitForGnpSNP.getOccurrence() + 1
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80
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81 def formatAlleles2GnpSnp(self):
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82 if self.getVar().find("-") != -1:
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83 self._polymType = "DELETION"
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84 self._gnpSnp_position = int(self._position) + 1
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85 self._gnpSnp_ref = self._var[1:]
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86 self._gnpSnp_var = "-" * len(self._gnpSnp_ref)
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87 self._polymLength = len(self._gnpSnp_ref)
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88 elif self.getVar().find("+") != -1:
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89 self._polymType = "INSERTION"
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90 self._gnpSnp_position = int(self._position)
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91 self._gnpSnp_var = self._var[1:]
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92 self._gnpSnp_ref = "-" * len(self._gnpSnp_var)
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93 self._polymLength = 1
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94 else:
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95 self._polymType = "SNP"
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96 self._gnpSnp_position = int(self._position)
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97 self._gnpSnp_var = self._var
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98 self._gnpSnp_ref = self._ref
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99 self._polymLength = 1
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100
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101 def setReads1(self, nbReadsLikeRef):
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102 self._reads1 = nbReadsLikeRef
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103
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104 def setReads2(self, nbReadsLikeVar):
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105 self._reads2 = nbReadsLikeVar
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106
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107 def setVarFreq(self, frequencyOfVariantAllele):
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108 frequencyOfVariantAllele = frequencyOfVariantAllele.replace("%","")
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109 frequencyOfVariantAllele = frequencyOfVariantAllele.replace(",",".")
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110 self._varFreq = float(frequencyOfVariantAllele)
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111
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112 def setStrands1(self, strandsOfReferenceAllele):
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113 self._strands1 = strandsOfReferenceAllele
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114
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115 def setStrands2(self, strandsOfVariantAllele):
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116 self._strands2 = strandsOfVariantAllele
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117
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118 def setQual1(self, averageQualityOfRef):
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119 self._qual1 = averageQualityOfRef
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120
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121 def setQual2(self, averageQualityOfVar):
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122 self._qual2 = averageQualityOfVar
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123
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124 def setPvalue(self, pvalue):
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125 self._pvalue = pvalue
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126
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127 def set5flank(self, s5flank):
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128 self._5flank = s5flank
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129
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130 def set3flank(self, s3flank):
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131 self._3flank = s3flank
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132
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133 def setGnpSNPRef(self, ref):
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134 self._gnpSnp_ref = ref
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135
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136 def setGnpSNPVar(self, var):
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137 self._gnpSnp_var = var
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138
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139 def setGnpSNPPosition(self, position):
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140 self._gnpSnp_position = position
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141
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142 def setOccurrence(self, occurrence):
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143 self._occurrence = occurrence
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144
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145 def setPolymType(self, polymType):
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146 self._polymType = polymType
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147
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148 def setPolymLength(self, polymLength):
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149 self._polymLength = polymLength
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150
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151 def getReads1(self):
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152 return self._reads1
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153
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154 def getReads2(self):
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155 return self._reads2
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156
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157 def getVarFreq(self):
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158 return self._varFreq
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159
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160 def getStrands1(self):
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161 return self._strands1
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162
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163 def getStrands2(self):
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164 return self._strands2
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165
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166 def getQual1(self):
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167 return self._qual1
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168
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169 def getQual2(self):
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170 return self._qual2
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171
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172 def getPvalue(self):
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173 return self._pvalue
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174
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175 def get5flank(self):
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176 return self._5flank
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177
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178 def get3flank(self):
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179 return self._3flank
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180
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181 def getPolymType(self):
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182 return self._polymType
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183
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184 def getGnpSnpVar(self):
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185 return self._gnpSnp_var
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186
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187 def getGnpSnpRef(self):
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188 return self._gnpSnp_ref
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189
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190 def getGnpSnpPosition(self):
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191 return self._gnpSnp_position
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192
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193 def getPolymLength(self):
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194 return self._polymLength
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195
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196 def getOccurrence(self):
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197 return self._occurrence
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198
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199 def setAttributes(self, lResults, iCurrentLineNumber):
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200 VarscanHit.setAttributes(self, lResults, iCurrentLineNumber)
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201 if lResults[4] != '':
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202 self.setReads1(lResults[4])
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203 else:
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204 raise CheckerException ("The field Reads1 is empty in varscan file in line %s" % (iCurrentLineNumber))
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205 if lResults[5] != '':
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206 self.setReads2(lResults[5])
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207 else:
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208 raise CheckerException ("The field Reads2 is empty in varscan file in line %s" % (iCurrentLineNumber))
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209 if lResults[6] != '' and re.match("[0-9\,\%]+", lResults[6]):
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210 self.setVarFreq(lResults[6])
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211 else:
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212 raise CheckerException ("The field VarFreq is empty or in bad format in varscan file in line %s" % (iCurrentLineNumber))
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213 if lResults[7] != '':
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214 self.setStrands1(lResults[7])
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215 else:
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216 raise CheckerException ("The field Strands1 is empty in varscan file in line %s" % (iCurrentLineNumber))
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217 if lResults[8] != '':
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218 self.setStrands2(lResults[8])
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219 else:
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220 raise CheckerException ("The field Strands2 is empty in varscan file in line %s" % (iCurrentLineNumber))
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221 if lResults[9] != '':
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222 self.setQual1(lResults[9])
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223 else:
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224 raise CheckerException ("The field Qual1 is empty in varscan file in line %s" % (iCurrentLineNumber))
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225 if lResults[10] != '':
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226 self.setQual2(lResults[10])
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227 else:
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228 raise CheckerException ("The field Qual2 is empty in varscan file in line %s" % (iCurrentLineNumber))
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229 if lResults[11] != '':
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230 self.setPvalue(lResults[11])
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231 else:
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232 raise CheckerException ("The field Pvalue is empty in varscan file in line %s" % (iCurrentLineNumber)) |
