Mercurial > repos > yufei-luo > s_mart
view commons/core/writer/SamWriter.py @ 39:1236e5a49595
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author | m-zytnicki |
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date | Mon, 13 May 2013 10:22:25 -0400 |
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. # import os import random from commons.core.writer.TranscriptListWriter import TranscriptListWriter class SamWriter(TranscriptListWriter): """ A class that writes a transcript list into a file with SAM format @ivar sizes: estimated sizes of the chromosomes @type sizes: dict of string to int """ def __init__(self, fileName, verbosity = 0): """ Constructor @param fileName: name of the file @type fileName: string @param verbosity: verbosity @type verbosity: int """ super(SamWriter, self).__init__(fileName, verbosity) self.sizes = {} self.headerWritten = False def close(self): """ Close file (trick to add header) """ super(SamWriter, self).close() if self.headerWritten: return tmpFileName = "tmpFile%d.sam" % (random.randint(0, 100000)) tmpHandle = open(tmpFileName, "w") for chromosome, size in self.sizes.iteritems(): tmpHandle.write("@SQ\tSN:%s\tLN:%d\n" % (chromosome, size)) self.handle = open(self.fileName) for line in self.handle: tmpHandle.write(line) tmpHandle.close() self.handle.close() os.rename(tmpFileName, self.fileName) self.headerWritten = True @staticmethod def getFileFormats(): """ Get the format of the file """ return ["sam"] @staticmethod def getExtension(): """ Get the usual extension for the file """ return "sam" def printTranscript(self, transcript): """ Export the given transcript with GBrowse format @param transcript: transcript to be printed @type transcript: class L{Transcript<Transcript>} @return: a string """ self.sizes[transcript.getChromosome()] = max(transcript.getEnd(), self.sizes.get(transcript.getChromosome(), 0)) return transcript.printSam()