Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/VarscanHit.py @ 38:2c0c0a89fad7
Uploaded
author | m-zytnicki |
---|---|
date | Thu, 02 May 2013 09:56:47 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/VarscanHit.py Thu May 02 09:56:47 2013 -0400 @@ -0,0 +1,175 @@ +# 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 + +class VarscanHit(object): + + def __init__(self, chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""): + self._chrom = chrom + self._position = position + self._ref = ref + self._var = var + self._readsRef = readsRef + self._readsVar = readsVar + self._varFreq = varFreq + self._strandsRef = strandsRef + self._strandsVar = strandsVar + self._qualRef = qualRef + self._qualVar = qualVar + self._pValue = pValue + + ## Equal operator + # + # @param o a VarscanFileAnalysis instance + # + def __eq__(self, o): + return self._chrom == o._chrom and self._position == o._position and self._ref == o._ref and self._var == o._var + + def setChrom(self, chromosome): + self._chrom = chromosome + + def setPosition(self, position): + self._position = position + + def setRef(self, referenceAllele): + self._ref = referenceAllele + + def setVar(self, variantAllele): + self._var = variantAllele + + def setReadsRef(self, readsRef): + self._readsRef = readsRef + + def setReadsVar(self, readsVar): + self._readsVar = readsVar + + def setVarFreq(self, varFreq): + self._varFreq = varFreq + + def setStrandsRef(self, strandsRef): + self._strandsRef = strandsRef + + def setStrandsVar(self, strandsVar): + self._strandsVar = strandsVar + + def setQualRef(self, qualRef): + self._qualRef = qualRef + + def setQualVar(self, qualVar): + self._qualVar = qualVar + + def setPValue(self, pValue): + self._pValue = pValue + + def getChrom(self): + return self._chrom + + def getPosition(self): + return self._position + + def getRef(self): + return self._ref + + def getVar(self): + return self._var + + def getReadsRef(self): + return self._readsRef + + def getReadsVar(self): + return self._readsVar + + def getVarFreq(self): + return self._varFreq + + def getStrandsRef(self): + return self._strandsRef + + def getStrandsVar(self): + return self._strandsVar + + def getQualRef(self): + return self._qualRef + + def getQualVar(self): + return self._qualVar + + def getPValue(self): + return self._pValue + + def getHeader(self): + return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\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\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()) + + 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.setVar(lResults[3]) + else: + raise CheckerException ("The field Var 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]) + + def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"): + varscanString = varscanString.rstrip() + lvarscanStringItem = varscanString.split(fieldSeparator) + if len(lvarscanStringItem)<12: + for i in range(len(lvarscanStringItem), 12): + lvarscanStringItem.append ("") + self.setAttributes(lvarscanStringItem, iCurrentLineNumber) \ No newline at end of file