view smart_toolShed/commons/core/writer/ @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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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
# "".
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# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
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# The fact that you are presently reading this means that you have had
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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):
        @param fileName: name of the file 
        @type fileName: string
        @param verbosity: verbosity
        @type verbosity: int
        self.fileName  = fileName
        self.verbosity = verbosity      = {-1: {}, 0: {}, 1: {}}
        self.title     = "Reads"
        self.strands   = False
        self.handle    = None

    def __del__(self):
        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
            for chromosome in sorted([strand]):
                 self.handle.write("variableStep chrom=%s%s\n" % (chromosome, strand2string[strand]))
                 for pos in sorted([strand][chromosome]):
                     self.handle.write("%d\t%d\n" % (pos,[strand][chromosome][pos]))

    def getFileFormats():
        Get the format of the file
        return ["wig", "wiggle"]
    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>}

    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[direction]:
  [direction][chromosome] = {}
        for exon in transcript.getExons():
            for pos in range(exon.getStart(), exon.getEnd()+1):
                if pos not in[direction][chromosome]:
          [direction][chromosome][pos]  = 1
          [direction][chromosome][pos] += 1