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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_v2_2_8 import VarscanHit_v2_2_8
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34 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag
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35
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36 class VarscanHit_v2_2_8_WithTag(VarscanHit_v2_2_8):
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37
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38 def __init__(self, chrom = "", position = "", ref = "", cns = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = "", mapQualRef = "", mapQualVar = "", readsRefPlus = "", readsRefMinus = "", readsVarPlus = "", readsVarMinus = "", var = "", tag = ""):
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39 self._tag = tag
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40 VarscanHit_v2_2_8.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue, mapQualRef, mapQualVar, readsRefPlus, readsRefMinus, readsVarPlus, readsVarMinus, var)
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41
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42 def __eq__(self, o):
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43 if self._tag == o._tag:
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44 return VarscanHit_v2_2_8.__eq__(self, o)
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45 return False
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46
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47 def setTag(self, tag):
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48 self._tag = tag
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49
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50 def getTag(self):
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51 return self._tag
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52
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53 def getHeader(self):
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54 return "Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\tTag\n"
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55
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56 def getVarscanLine(self):
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57 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\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(), self.getTag())
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58
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59 def setAttributes(self, lResults, iCurrentLineNumber):
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60 VarscanHit_v2_2_8.setAttributes(self, lResults, iCurrentLineNumber)
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61 if lResults[19] != '':
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62 self.setTag(lResults[19])
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63 else:
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64 raise CheckerException ("The field tag is empty in varscan file in line %s" % iCurrentLineNumber)
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65
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66 def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
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67 varscanString = varscanString.rstrip()
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68 lvarscanStringItem = varscanString.split(fieldSeparator)
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69 if len(lvarscanStringItem) < 20:
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70 raise CheckerException ("This varscan line (l.%s) is not complete" % iCurrentLineNumber)
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71 self.setAttributes(lvarscanStringItem, iCurrentLineNumber)
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72
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73 def convertVarscanHit_v2_2_8_WithTag_To_VarscanHit_WithTag(self):
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74 iVarscanHit = VarscanHit_WithTag()
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75 iVarscanHit.setChrom(self.getChrom())
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76 iVarscanHit.setPosition(self.getPosition())
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77 iVarscanHit.setRef(self.getRef())
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78 iVarscanHit.setVar(self.getVar())
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79 iVarscanHit.setReadsRef(self.getReadsRef())
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80 iVarscanHit.setReadsVar(self.getReadsVar())
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81 iVarscanHit.setVarFreq(self.getVarFreq())
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82 iVarscanHit.setStrandsRef(self.getStrandsRef())
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83 iVarscanHit.setStrandsVar(self.getStrandsVar())
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84 iVarscanHit.setQualRef(self.getQualRef())
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85 iVarscanHit.setQualVar(self.getQualVar())
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86 iVarscanHit.setPValue(self.getPValue())
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87 iVarscanHit.setTag(self.getTag())
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88 return iVarscanHit |