Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/VarscanHit_v2_2_8.py @ 42:2abc37c27164
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author | m-zytnicki |
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date | Wed, 18 Sep 2013 07:45:59 -0400 |
parents | 769e306b7933 |
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# Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. from commons.core.checker.CheckerException import CheckerException from commons.core.parsing.VarscanHit import VarscanHit class VarscanHit_v2_2_8(VarscanHit): def __init__(self, chrom = "", position = "", ref = "", cns = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = "", mapQualRef = "", mapQualVar = "", readsRefPlus = "", readsRefMinus = "", readsVarPlus = "", readsVarMinus = "", var = ""): self._cns = cns self._mapQualRef = mapQualRef self._mapQualVar = mapQualVar self._readsRefPlus = readsRefPlus self._readsRefMinus = readsRefMinus self._readsVarPlus = readsVarPlus self._readsVarMinus = readsVarMinus VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue) ## Equal operator # # @param o a VarscanFileAnalysis instance # def __eq__(self, o): if self._cns == o._cns: return VarscanHit.__eq__(self, o) return False def setCns(self, consensus): self._cns = consensus def setMapQualRef(self, mapQualRef): self._mapQualRef = mapQualRef def setMapQualVar(self, mapQualVar): self._mapQualVar = mapQualVar def setReadsRefPlus(self, readsRefPlus): self._readsRefPlus = readsRefPlus def setReadsRefMinus(self, readsRefMinus): self._readsRefMinus = readsRefMinus def setReadsVarPlus(self, readsVarPlus): self._readsVarPlus = readsVarPlus def setReadsVarMinus(self, readsVarMinus): self._readsVarMinus = readsVarMinus def getCns(self): return self._cns def getMapQualRef(self): return self._mapQualRef def getMapQualVar(self): return self._mapQualVar def getReadsRefPlus(self): return self._readsRefPlus def getReadsRefMinus(self): return self._readsRefMinus def getReadsVarPlus(self): return self._readsVarPlus def getReadsVarMinus(self): return self._readsVarMinus def getHeader(self): return "Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\n" def getVarscanLine(self): 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()) def setAttributes(self, lResults, iCurrentLineNumber): if lResults[0] != '': self.setChrom(lResults[0]) else: raise CheckerException ("The field Chrom is empty in varscan file in line %s" % iCurrentLineNumber) if lResults[1] != '': self.setPosition(lResults[1]) else: raise CheckerException ("The field Position is empty in varscan file in line %s" % iCurrentLineNumber) if lResults[2] != '': self.setRef(lResults[2]) else: raise CheckerException ("The field Ref is empty in varscan file in line %s" % iCurrentLineNumber) if lResults[3] != '': self.setCns(lResults[3]) else: raise CheckerException ("The field Cons is empty in varscan file in line %s" % iCurrentLineNumber) if lResults[4] != '': self.setReadsRef(lResults[4]) if lResults[5] != '': self.setReadsVar(lResults[5]) if lResults[6] != '': self.setVarFreq(lResults[6]) if lResults[7] != '': self.setStrandsRef(lResults[7]) if lResults[8] != '': self.setStrandsVar(lResults[8]) if lResults[9] != '': self.setQualRef(lResults[9]) if lResults[10] != '': self.setQualVar(lResults[10]) if lResults[11] != '': self.setPValue(lResults[11]) if lResults[12] != '': self.setMapQualRef(lResults[12]) if lResults[13] != '': self.setMapQualVar(lResults[13]) if lResults[14] != '': self.setReadsRefPlus(lResults[14]) if lResults[15] != '': self.setReadsRefMinus(lResults[15]) if lResults[16] != '': self.setReadsVarPlus(lResults[16]) if lResults[17] != '': self.setReadsVarMinus(lResults[17]) if lResults[18] != '': self.setVar(lResults[18]) else: raise CheckerException ("The field varAllele is empty in varscan file in line %s" % iCurrentLineNumber) def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"): varscanString = varscanString.rstrip() lvarscanStringItem = varscanString.split(fieldSeparator) if len(lvarscanStringItem) < 19: raise CheckerException ("This varscan line (l.%s) is not complete" % iCurrentLineNumber) self.setAttributes(lvarscanStringItem, iCurrentLineNumber) def convertVarscanHit_v2_2_8_To_VarscanHit(self): iVarscanHit = VarscanHit() iVarscanHit.setChrom(self.getChrom()) iVarscanHit.setPosition(self.getPosition()) iVarscanHit.setRef(self.getRef()) iVarscanHit.setVar(self.getVar()) iVarscanHit.setReadsRef(self.getReadsRef()) iVarscanHit.setReadsVar(self.getReadsVar()) iVarscanHit.setVarFreq(self.getVarFreq()) iVarscanHit.setStrandsRef(self.getStrandsRef()) iVarscanHit.setStrandsVar(self.getStrandsVar()) iVarscanHit.setQualRef(self.getQualRef()) iVarscanHit.setQualVar(self.getQualVar()) iVarscanHit.setPValue(self.getPValue()) return iVarscanHit