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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
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34 class VarscanHit(object):
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35
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36 def __init__(self, chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""):
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37 self._chrom = chrom
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38 self._position = position
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39 self._ref = ref
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40 self._var = var
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41 self._readsRef = readsRef
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42 self._readsVar = readsVar
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43 self._varFreq = varFreq
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44 self._strandsRef = strandsRef
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45 self._strandsVar = strandsVar
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46 self._qualRef = qualRef
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47 self._qualVar = qualVar
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48 self._pValue = pValue
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49
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50 ## Equal operator
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51 #
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52 # @param o a VarscanFileAnalysis instance
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53 #
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54 def __eq__(self, o):
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55 return self._chrom == o._chrom and self._position == o._position and self._ref == o._ref and self._var == o._var
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56
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57 def setChrom(self, chromosome):
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58 self._chrom = chromosome
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59
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60 def setPosition(self, position):
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61 self._position = position
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62
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63 def setRef(self, referenceAllele):
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64 self._ref = referenceAllele
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65
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66 def setVar(self, variantAllele):
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67 self._var = variantAllele
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68
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69 def setReadsRef(self, readsRef):
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70 self._readsRef = readsRef
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71
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72 def setReadsVar(self, readsVar):
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73 self._readsVar = readsVar
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74
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75 def setVarFreq(self, varFreq):
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76 self._varFreq = varFreq
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77
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78 def setStrandsRef(self, strandsRef):
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79 self._strandsRef = strandsRef
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80
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81 def setStrandsVar(self, strandsVar):
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82 self._strandsVar = strandsVar
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83
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84 def setQualRef(self, qualRef):
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85 self._qualRef = qualRef
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86
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87 def setQualVar(self, qualVar):
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88 self._qualVar = qualVar
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89
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90 def setPValue(self, pValue):
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91 self._pValue = pValue
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92
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93 def getChrom(self):
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94 return self._chrom
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95
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96 def getPosition(self):
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97 return self._position
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98
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99 def getRef(self):
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100 return self._ref
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101
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102 def getVar(self):
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103 return self._var
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104
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105 def getReadsRef(self):
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106 return self._readsRef
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107
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108 def getReadsVar(self):
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109 return self._readsVar
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110
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111 def getVarFreq(self):
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112 return self._varFreq
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113
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114 def getStrandsRef(self):
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115 return self._strandsRef
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116
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117 def getStrandsVar(self):
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118 return self._strandsVar
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119
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120 def getQualRef(self):
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121 return self._qualRef
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122
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123 def getQualVar(self):
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124 return self._qualVar
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125
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126 def getPValue(self):
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127 return self._pValue
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128
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129 def getHeader(self):
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130 return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\n"
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131
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132 def getVarscanLine(self):
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133 return "%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.getVar(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(), self.getQualRef(), self.getQualVar(), self.getPValue())
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134
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135 def setAttributes(self, lResults, iCurrentLineNumber):
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136 if lResults[0] != '':
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137 self.setChrom(lResults[0])
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138 else:
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139 raise CheckerException ("The field Chrom is empty in varscan file in line %s" % iCurrentLineNumber)
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140 if lResults[1] != '':
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141 self.setPosition(lResults[1])
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142 else:
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143 raise CheckerException ("The field Position is empty in varscan file in line %s" % iCurrentLineNumber)
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144 if lResults[2] != '':
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145 self.setRef(lResults[2])
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146 else:
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147 raise CheckerException ("The field Ref is empty in varscan file in line %s" % iCurrentLineNumber)
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148 if lResults[3] != '':
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149 self.setVar(lResults[3])
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150 else:
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151 raise CheckerException ("The field Var is empty in varscan file in line %s" % iCurrentLineNumber)
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152 if lResults[4] != '':
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153 self.setReadsRef(lResults[4])
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154 if lResults[5] != '':
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155 self.setReadsVar(lResults[5])
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156 if lResults[6] != '':
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157 self.setVarFreq(lResults[6])
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158 if lResults[7] != '':
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159 self.setStrandsRef(lResults[7])
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160 if lResults[8] != '':
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161 self.setStrandsVar(lResults[8])
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162 if lResults[9] != '':
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163 self.setQualRef(lResults[9])
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164 if lResults[10] != '':
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165 self.setQualVar(lResults[10])
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166 if lResults[11] != '':
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167 self.setPValue(lResults[11])
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168
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169 def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
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170 varscanString = varscanString.rstrip()
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171 lvarscanStringItem = varscanString.split(fieldSeparator)
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172 if len(lvarscanStringItem)<12:
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173 for i in range(len(lvarscanStringItem), 12):
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174 lvarscanStringItem.append ("")
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175 self.setAttributes(lvarscanStringItem, iCurrentLineNumber) |
