view smart_toolShed/commons/core/writer/EmblWriter.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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# modify and/ or redistribute the software under the terms of the CeCILL
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from commons.core.writer.TranscriptListWriter import TranscriptListWriter


class EmblWriter(TranscriptListWriter):
    """
    A class that writes a transcript list into several files with EMBL format
    @ivar fileName: name of the file 
    @type fileName: string
    @ivar handle: handle to the file
    @type handle: file handle
    """


    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.handles = {}
        self.handle = None


    def __del__(self):
        """
        Destructor
        Trick to append the sequences at the end of the EMBL files
        """
        handle                = open(self.sequenceFileName)
        currentHandle = None
        for line in handle:
            if line[0] == ">":
                chromosome = line[1:].strip()
                if chromosome in self.handles:
                    currentHandle = self.handles[chromosome]
                else:
                    currentHandle = None
            else:
                if currentHandle != None:
                    currentHandle.write(line)
        handle.close()
        for handle in self.handles.values():
            handle.close()
            

    @staticmethod
    def getFileFormats():
        """
        Get the format of the file
        """
        return ["embl"]
        
        
    @staticmethod
    def getExtension():
        """
        Get the usual extension for the file
        """
        return "embl"


    def addTranscript(self, transcript):
        """
        Add a transcript to the list of transcripts to be written
        @param transcript: transcript to be written
        @type    transcript: class L{Transcript<Transcript>}
        """
        chromosome = transcript.getChromosome()
        if chromosome not in self.handles:
            self.handles[chromosome] = open("%s%s.embl" % (self.fileName[:-len(".embl")], chromosome.title()), "w")
        self.handles[chromosome].write(self.printTranscript(transcript))


    def printTranscript(self, transcript):
        """
        Export the given transcript with GFF2 format
        @param transcript: transcript to be printed
        @type transcript: class L{Transcript<Transcript>}
        @return: a string
        """
        return transcript.printEmbl()