Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/VarscanHit_v2_2_8_WithTag.py @ 27:4e7ee5683ef1
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:30:11 -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_v2_2_8 import VarscanHit_v2_2_8 from commons.core.parsing.VarscanHit_WithTag import VarscanHit_WithTag class VarscanHit_v2_2_8_WithTag(VarscanHit_v2_2_8): def __init__(self, chrom = "", position = "", ref = "", cns = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = "", mapQualRef = "", mapQualVar = "", readsRefPlus = "", readsRefMinus = "", readsVarPlus = "", readsVarMinus = "", var = "", tag = ""): self._tag = tag 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) def __eq__(self, o): if self._tag == o._tag: return VarscanHit_v2_2_8.__eq__(self, o) return False def setTag(self, tag): self._tag = tag def getTag(self): return self._tag def getHeader(self): return "Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\tTag\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\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()) def setAttributes(self, lResults, iCurrentLineNumber): VarscanHit_v2_2_8.setAttributes(self, lResults, iCurrentLineNumber) if lResults[19] != '': self.setTag(lResults[19]) else: raise CheckerException ("The field tag 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) < 20: raise CheckerException ("This varscan line (l.%s) is not complete" % iCurrentLineNumber) self.setAttributes(lvarscanStringItem, iCurrentLineNumber) def convertVarscanHit_v2_2_8_WithTag_To_VarscanHit_WithTag(self): iVarscanHit = VarscanHit_WithTag() 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()) iVarscanHit.setTag(self.getTag()) return iVarscanHit