Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/VarscanFileForGnpSNP.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.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