Mercurial > repos > yufei-luo > s_mart
diff commons/core/writer/SamWriter.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/SamWriter.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,101 @@ +# +# 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() +