Mercurial > repos > yufei-luo > s_mart
diff commons/core/writer/WriterChooser.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/writer/WriterChooser.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,127 @@ +# +# 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.writer.TranscriptListWriter import TranscriptListWriter +from commons.core.writer.SequenceListWriter import SequenceListWriter +from commons.core.writer.BedWriter import BedWriter +from commons.core.writer.CsvWriter import CsvWriter +from commons.core.writer.EmblWriter import EmblWriter +from commons.core.writer.FastaWriter import FastaWriter +from commons.core.writer.FastqWriter import FastqWriter +from commons.core.writer.GbWriter import GbWriter +from commons.core.writer.Gff2Writer import Gff2Writer +from commons.core.writer.SamWriter import SamWriter +from commons.core.writer.UcscWriter import UcscWriter +from commons.core.writer.WigWriter import WigWriter +from commons.core.writer.Gff3Writer import Gff3Writer +from commons.core.writer.GtfWriter import GtfWriter +from commons.core.writer.MapWriter import MapWriter + + +class WriterChooser(object): + """ + A class that finds the correct writer + @ivar type: transcript / sequence writer + @type type: string + @ivar format: the format of the writer + @type format: string + @ivar writerClass: the class of the writer + @type writerClass: string + @ivar extension: default extension of the file + @type extension: string + @ivar verbosity: verbosity + @type verbosity: int + """ + + def __init__(self, verbosity = 0): + """ + Constructor + @param verbosity: verbosity + @type verbosity: int + """ + self.type = None + self.format = None + self.writerClass = None + self.extension = None + self.verbosity = verbosity + + + def findFormat(self, format, type = None): + """ + Find the correct parser + @ivar format: the format + @type format: string + @ivar type: transcript sequence parser (None is all) + @type type: string + @return: a parser + """ + classes = {} + if (type == "transcript"): + classes = {TranscriptListWriter: "transcript"} + elif (type == "sequence"): + classes = {SequenceListWriter: "sequence"} + elif (type == None): + classes = {TranscriptListWriter: "transcript", SequenceListWriter: "sequence"} + else: + sys.exit("Do not understand format type '%s'" % (type)) + + for classType in classes: + for writerClass in classType.__subclasses__(): + if format in writerClass.getFileFormats(): + self.writerClass = writerClass + self.extension = writerClass.getExtension() + self.type = classes[classType] + return + sys.exit("Cannot get writer for format '%s'" % (format)) + + + def getWriter(self, fileName): + """ + Get the writer previously found + @return: the writer + """ + return self.writerClass(fileName, self.verbosity) + + + def getType(self): + """ + Get the type of writer previously found + @return: the type of writer + """ + return self.type + + + def getExtension(self): + """ + Get the default extension of writer previously found + @return: the extension + """ + return self.extension +