Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/VarscanHit.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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175 self.setAttributes(lvarscanStringItem, iCurrentLineNumber) |