Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/VarscanHitForGnpSNP.py @ 14:c79b9ae3f65f
Deleted selected files
author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -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 import VarscanHit import re class VarscanHitForGnpSNP(VarscanHit): def __init__(self): VarscanHit.__init__(self) self._reads1 = '' self._reads2 = '' self._varFreq = '' self._strands1 = '' self._strands2 = '' self._qual1 = '' self._qual2 = '' self._pvalue = '' self._5flank = '' self._3flank = '' self._gnpSnp_ref = '' self._gnpSnp_var = '' self._gnpSnp_position = 0 self._polymType = '' self._polymLength = 0 self._occurrence = 1 ## Equal operator # # @param o a VarscanFileAnalysis instance # def __eq__(self, o): return VarscanHit.__eq__(self, o) \ and self._reads1 == o._reads1 and self._reads2 == o._reads2 \ and self._varFreq == o._varFreq and self._strands1 == o._strands1 \ and self._strands2 == o._strands2 and self._qual1 == o._qual1 \ and self._qual2 == o._qual2 and self._pvalue == o._pvalue \ and self._3flank == o._3flank and self._5flank == o._5flank \ and self._gnpSnp_position == o._gnpSnp_position and self._gnpSnp_ref == o._gnpSnp_ref \ and self._gnpSnp_var == o._gnpSnp_var and self._polymLength == o._polymLength \ and self._polymType == o._polymType and self._occurrence == o._occurrence def isPolymTypeAlreadyFoundAtThisChromAndThisPosition(self, iVarscanHitForGnpSNP): return self._chrom == iVarscanHitForGnpSNP.getChrom() \ and self._position == iVarscanHitForGnpSNP.getPosition() \ and self._polymType == iVarscanHitForGnpSNP.getPolymType() def manageOccurrence(self, iVarscanHitForGnpSNP=None): if iVarscanHitForGnpSNP != None and self.isPolymTypeAlreadyFoundAtThisChromAndThisPosition(iVarscanHitForGnpSNP): self._occurrence = iVarscanHitForGnpSNP.getOccurrence() + 1 def formatAlleles2GnpSnp(self): if self.getVar().find("-") != -1: self._polymType = "DELETION" self._gnpSnp_position = int(self._position) + 1 self._gnpSnp_ref = self._var[1:] self._gnpSnp_var = "-" * len(self._gnpSnp_ref) self._polymLength = len(self._gnpSnp_ref) elif self.getVar().find("+") != -1: self._polymType = "INSERTION" self._gnpSnp_position = int(self._position) self._gnpSnp_var = self._var[1:] self._gnpSnp_ref = "-" * len(self._gnpSnp_var) self._polymLength = 1 else: self._polymType = "SNP" self._gnpSnp_position = int(self._position) self._gnpSnp_var = self._var self._gnpSnp_ref = self._ref self._polymLength = 1 def setReads1(self, nbReadsLikeRef): self._reads1 = nbReadsLikeRef def setReads2(self, nbReadsLikeVar): self._reads2 = nbReadsLikeVar def setVarFreq(self, frequencyOfVariantAllele): frequencyOfVariantAllele = frequencyOfVariantAllele.replace("%","") frequencyOfVariantAllele = frequencyOfVariantAllele.replace(",",".") self._varFreq = float(frequencyOfVariantAllele) def setStrands1(self, strandsOfReferenceAllele): self._strands1 = strandsOfReferenceAllele def setStrands2(self, strandsOfVariantAllele): self._strands2 = strandsOfVariantAllele def setQual1(self, averageQualityOfRef): self._qual1 = averageQualityOfRef def setQual2(self, averageQualityOfVar): self._qual2 = averageQualityOfVar def setPvalue(self, pvalue): self._pvalue = pvalue def set5flank(self, s5flank): self._5flank = s5flank def set3flank(self, s3flank): self._3flank = s3flank def setGnpSNPRef(self, ref): self._gnpSnp_ref = ref def setGnpSNPVar(self, var): self._gnpSnp_var = var def setGnpSNPPosition(self, position): self._gnpSnp_position = position def setOccurrence(self, occurrence): self._occurrence = occurrence def setPolymType(self, polymType): self._polymType = polymType def setPolymLength(self, polymLength): self._polymLength = polymLength def getReads1(self): return self._reads1 def getReads2(self): return self._reads2 def getVarFreq(self): return self._varFreq def getStrands1(self): return self._strands1 def getStrands2(self): return self._strands2 def getQual1(self): return self._qual1 def getQual2(self): return self._qual2 def getPvalue(self): return self._pvalue def get5flank(self): return self._5flank def get3flank(self): return self._3flank def getPolymType(self): return self._polymType def getGnpSnpVar(self): return self._gnpSnp_var def getGnpSnpRef(self): return self._gnpSnp_ref def getGnpSnpPosition(self): return self._gnpSnp_position def getPolymLength(self): return self._polymLength def getOccurrence(self): return self._occurrence def setAttributes(self, lResults, iCurrentLineNumber): VarscanHit.setAttributes(self, lResults, iCurrentLineNumber) if lResults[4] != '': self.setReads1(lResults[4]) else: raise CheckerException ("The field Reads1 is empty in varscan file in line %s" % (iCurrentLineNumber)) if lResults[5] != '': self.setReads2(lResults[5]) else: raise CheckerException ("The field Reads2 is empty in varscan file in line %s" % (iCurrentLineNumber)) if lResults[6] != '' and re.match("[0-9\,\%]+", lResults[6]): self.setVarFreq(lResults[6]) else: raise CheckerException ("The field VarFreq is empty or in bad format in varscan file in line %s" % (iCurrentLineNumber)) if lResults[7] != '': self.setStrands1(lResults[7]) else: raise CheckerException ("The field Strands1 is empty in varscan file in line %s" % (iCurrentLineNumber)) if lResults[8] != '': self.setStrands2(lResults[8]) else: raise CheckerException ("The field Strands2 is empty in varscan file in line %s" % (iCurrentLineNumber)) if lResults[9] != '': self.setQual1(lResults[9]) else: raise CheckerException ("The field Qual1 is empty in varscan file in line %s" % (iCurrentLineNumber)) if lResults[10] != '': self.setQual2(lResults[10]) else: raise CheckerException ("The field Qual2 is empty in varscan file in line %s" % (iCurrentLineNumber)) if lResults[11] != '': self.setPvalue(lResults[11]) else: raise CheckerException ("The field Pvalue is empty in varscan file in line %s" % (iCurrentLineNumber))