Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/ParserChooser.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
children | 94ab73e8a190 |
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# # Copyright INRA-URGI 2009-2010 # # 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. # import sys from commons.core.parsing.TranscriptListParser import TranscriptListParser from commons.core.parsing.MapperParser import MapperParser from commons.core.parsing.SequenceListParser import SequenceListParser from commons.core.parsing.BedParser import BedParser from commons.core.parsing.GffParser import GffParser from commons.core.parsing.MapperParser import MapperParser from commons.core.parsing.CoordsParser import CoordsParser from commons.core.parsing.SeqmapParser import SeqmapParser from commons.core.parsing.SoapParser import SoapParser from commons.core.parsing.Soap2Parser import Soap2Parser from commons.core.parsing.BlastParser import BlastParser from commons.core.parsing.PslParser import PslParser from commons.core.parsing.RmapParser import RmapParser from commons.core.parsing.ShrimpParser import ShrimpParser from commons.core.parsing.AxtParser import AxtParser from commons.core.parsing.ExoParser import ExoParser from commons.core.parsing.MaqParser import MaqParser from commons.core.parsing.SamParser import SamParser from commons.core.parsing.BamParser import BamParser from commons.core.parsing.BowtieParser import BowtieParser from commons.core.parsing.ElandParser import ElandParser from commons.core.parsing.GtfParser import GtfParser from commons.core.parsing.FastaParser import FastaParser from commons.core.parsing.FastqParser import FastqParser from commons.core.parsing.MapParser import MapParser from commons.core.parsing.NCListParser import NCListParser from commons.core.parsing.PklParser import PklParser #Attention!! Do not delete the imports!! They are used to know the type of file format!!! class ParserChooser(object): """ A class that finds the correct parser @ivar format: the format @type format: string @ivar type: transcript / mapping / sequence parser @type type: string @ivar parser: the parser @type parser: object @ivar verbosity: verbosity @type verbosity: int """ def __init__(self, verbosity = 0): """ Constructor @param verbosity: verbosity @type verbosity: int """ self.type = None self.parserClass = None self.verbosity = verbosity def findFormat(self, format, type = None): """ Find the correct parser @ivar format: the format @type format: string @ivar type: transcript / mapping / sequence parser (None is all) @type type: string @return: a parser """ classes = {} if (type == "transcript"): classes = {TranscriptListParser: "transcript"} elif (type == "mapping"): classes = {MapperParser: "mapping"} elif (type == "sequence"): classes = {SequenceListParser: "sequence"} elif (type == None): classes = {TranscriptListParser: "transcript", MapperParser: "mapping", SequenceListParser: "sequence"} else: raise Exception("Do not understand format type '%s'" % (type)) for classType in classes: for parserClass in classType.__subclasses__(): if format in parserClass.getFileFormats(): self.parserClass = parserClass self.type = classes[classType] return raise Exception("Cannot get parser for format '%s'" % (format)) def getParser(self, fileName): """ Get the parser previously found @return: the parser """ return self.parserClass(fileName, self.verbosity) def getType(self): """ Get the type of parser previously found @return: the type of parser """ return self.type