view smart_toolShed/commons/core/writer/ @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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
# "".
# 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.writer.TranscriptListWriter import TranscriptListWriter

class GtfWriter(TranscriptListWriter):
    A class that writes a transcript list into a file with GTF format
    @ivar fileName: name of the file 
    @type fileName: string
    @ivar handle: handle to the file
    @type handle: file handle

    def __init__(self, fileName, verbosity = 0):
        @param fileName: name of the file 
        @type fileName: string
        @param verbosity: verbosity
        @type verbosity: int
        self.header = ""
        self.title    = "S-MART"
        super(GtfWriter, self).__init__(fileName, verbosity)

    def getFileFormats():
        Get the format of the file
        return ["gtf", "gtf2"]
    def getExtension():
        Get the usual extension for the file
        return "gtf"
    def setTitle(self, title):
        Set the title of the transcripts
        @param title: the title of the transcripts
        @type    title: string
        self.title = title

    def printTranscript(self, transcript):
        Export the given transcript with GTF format
        @param transcript: transcript to be printed
        @type transcript: class L{Transcript<Transcript>}
        @return: a string
        return transcript.printGtf(self.title)