Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/VarscanFileForGnpSNP.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/VarscanFileForGnpSNP.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,72 @@ +# 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.parsing.VarscanHitForGnpSNP import VarscanHitForGnpSNP +from commons.core.parsing.VarscanFile import VarscanFile + +class VarscanFileForGnpSNP(VarscanFile): + + def __init__(self, varscanFileName, fastqFileName="", refFastaFileName="", taxonName=""): + VarscanFile.__init__(self, varscanFileName) + self._fastqFileName = fastqFileName + self._refFastaFileName = refFastaFileName + self._taxonName = taxonName + self._previousVarscanHit = None + + ## Equal operator + # + # @param o a VarscanFileAnalysis instance + # + def __eq__(self, o): + return VarscanFile.__eq__(self, o) and self._fastqFileName == o._fastqFileName \ + and self._refFastaFileName == o._refFastaFileName and self._taxonName == o._taxonName + + def getVarscanFieldSeparator(self): + return self._varscanFieldSeparator + + def getFastqFileName(self): + return self._fastqFileName + + def getRefFastaFileName(self): + return self._refFastaFileName + + def getTaxonName(self): + return self._taxonName + + def createVarscanHit(self, line, currentLineNumber): + line = line.strip() + lResults = line.split(self._varscanFieldSeparator) + iVarscanHit = VarscanHitForGnpSNP() + iVarscanHit.setAttributes(lResults, currentLineNumber) + iVarscanHit.formatAlleles2GnpSnp() + iVarscanHit.manageOccurrence(self._previousVarscanHit) + self._previousVarscanHit = iVarscanHit + return iVarscanHit