Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/VarscanHit_v2_2_8_WithTag.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/VarscanHit_v2_2_8_WithTag.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,88 @@ +# 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 \ No newline at end of file