annotate smart_toolShed/commons/core/writer/SamWriter.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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# Copyright INRA-URGI 2009-2010
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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()