Mercurial > repos > yufei-luo > s_mart
view commons/core/writer/GbWriter.py @ 8:4dded8b1fbc4
Deleted selected files
author | m-zytnicki |
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date | Fri, 18 Jan 2013 09:01:47 -0500 |
parents | 769e306b7933 |
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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. # from commons.core.writer.TranscriptListWriter import TranscriptListWriter class GbWriter(TranscriptListWriter): """ A class that writes a transcript list into a file with GBrowse format @ivar fileName: name of the file @type fileName: string @ivar handle: handle to the file @type handle: file handle @ivar header: first lines of the file @type header: string """ def __init__(self, fileName, verbosity = 0): """ Constructor @param fileName: name of the file @type fileName: string @param verbosity: verbosity @type verbosity: int """ self.header = "[READS]\nbgcolor = red\nstrand_arrow = 1\n\n" super(GbWriter, self).__init__(fileName, verbosity) @staticmethod def getFileFormats(): """ Get the format of the file """ return ["gb", "gbrowse"] @staticmethod def getExtension(): """ Get the usual extension for the file """ return "gb" def setColor(self, color): """ Set the color of the track @param color: the color of the track @type color: string """ if color != None: self.header = "[READS]\nbgcolor= %s\nstrand_arrow = 1\n\n" % (color) def copyProperties(self, gbParser): """ Copy the properties collected by a parser, to produce a similar output @param gbParser: a GBrowse parser @type gbParser: class L{GbParser<GbParser>} """ self.setColor(gbParser.color) def printTranscript(self, transcript): """ Export the given transcript with GBrowse format Possibly skip the reference if already put @param transcript: transcript to be printed @type transcript: class L{Transcript<Transcript>} @return: a string """ if self.lastChromosome != None and self.lastChromosome == transcript.getChromosome(): return transcript.printGBrowseLine() return transcript.printGBrowse()