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

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

#
# Copyright INRA-URGI 2009-2010
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from commons.core.writer.TranscriptListWriter import TranscriptListWriter


class WigWriter(TranscriptListWriter):
    """
    A class that writes a transcript list into a file with WIGGLE 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.fileName  = fileName
        self.verbosity = verbosity
        self.data      = {-1: {}, 0: {}, 1: {}}
        self.title     = "Reads"
        self.strands   = False
        self.handle    = None


    def __del__(self):
        """
        Destructor
        Actually print the file
        """
        strand2string = {-1: "-", 1: "+", 0: ""}
        self.handle   = open(self.fileName, "w")
        self.handle.write("track type=wiggle_0 name=\"%s\"\n" % (self.title))
        for strand in self.data:
            for chromosome in sorted(self.data[strand]):
                 self.handle.write("variableStep chrom=%s%s\n" % (chromosome, strand2string[strand]))
                 for pos in sorted(self.data[strand][chromosome]):
                     self.handle.write("%d\t%d\n" % (pos, self.data[strand][chromosome][pos]))
        self.handle.close()

        
    @staticmethod
    def getFileFormats():
        """
        Get the format of the file
        """
        return ["wig", "wiggle"]
        
        
    @staticmethod
    def getExtension():
        """
        Get the usual extension for the file
        """
        return "wig"
        
        
    def setTitle(self, title):
        """
        Set the title of the track
        @param title: the title of the track
        @type    title: string
        """
        if title != None:
            self.title = title


    def setStrands(self, strands):
        """
        Consider each strand separately
        @param boolean: whether each strand should be considered separately
        @type  boolean: boolean
        """
        self.strands = strands


    def copyProperties(self, parser):
        """
        Copy the properties collected by a parser, to produce a similar output
        @param bedParser: a parser
        @type    bedParser: class L{TranscriptListWriter<TranscriptListWriter>}
        """
        self.setTitle(parser.title)
        

    def addTranscript(self, transcript):
        """
        Export the given transcript with GBrowse format
        @param transcript: transcript to be printed
        @type transcript: class L{Transcript<Transcript>}
        @return: a string
        """
        chromosome = transcript.getChromosome()
        direction  = transcript.getDirection()
        if not self.strands:
            direction = 0
        if chromosome not in self.data[direction]:
            self.data[direction][chromosome] = {}
        for exon in transcript.getExons():
            for pos in range(exon.getStart(), exon.getEnd()+1):
                if pos not in self.data[direction][chromosome]:
                    self.data[direction][chromosome][pos]  = 1
                else:
                    self.data[direction][chromosome][pos] += 1