Ejemplo n.º 1
0
    def __init__( self, input_gtf_false_path, data_gtf):

        super(Gtf, self).__init__()

        self.track = None

        self.input_gtf_false_path = input_gtf_false_path
        self.name_gtf = data_gtf["name"]
        self.priority = data_gtf["order_index"]

        #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)

        # TODO: See if we need these temporary files as part of the generated files
        genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
        unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")

        # GtfToGenePred
        subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)

        # TODO: From there, refactor because common use with Gff3.py
        #  genePredToBed processing
        subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)

        # Sort processing
        subtools.sort(unsortedBedFile.name, sortedBedFile.name)

        # bedToBigBed processing
        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
        trackName = "".join( ( self.name_gtf, ".bb") )
        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
        with open(myBigBedFilePath, 'w') as bigBedFile:
            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)

        # Create the Track Object
        self.createTrack(file_path=trackName,
                         track_name=trackName,
                         long_label=self.name_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
                         track_file=myBigBedFilePath)
        #
        # dataURL = "tracks/%s" % trackName
        #
        # trackDb = TrackDb(
        #     trackName=trackName,
        #     longLabel=self.name_gtf,
        #     shortLabel=self.getShortName( self.name_gtf ),
        #     trackDataURL=dataURL,
        #     trackType='bigBed 12 +',
        #     visibility='dense',
        #     priority=self.priority,
        # )
        # self.track = Track(
        #     trackFile=myBigBedFilePath,
        #     trackDb=trackDb,
        # )

        print("- Gtf %s created" % self.name_gtf)
Ejemplo n.º 2
0
    def __init__( self, inputBedGeneric, data_bed_generic):
        super(Bed, self).__init__()

        self.track = None

        self.inputBedGeneric = inputBedGeneric

        self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")

        self.data_bed_generic = data_bed_generic
        self.name_bed_generic = self.data_bed_generic["name"]
        self.priority = self.data_bed_generic["order_index"]

        # Sort processing
        subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)

        # bedToBigBed processing
        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
        trackName = "".join( ( self.name_bed_generic, ".bb") )

        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
        with open(myBigBedFilePath, 'w') as self.bigBedFile:
            subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name)

        # Create the Track Object
        self.createTrack(file_path=trackName,
                         track_name=trackName,
                         long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
                         priority=self.priority,
                         track_file=myBigBedFilePath)

        # dataURL = "tracks/%s" % trackName
        #
        # trackDb = TrackDb(
        #     trackName=trackName,
        #     longLabel=self.name_bed_generic,
        #     shortLabel=self.getShortName(self.name_bed_generic),
        #     trackDataURL=dataURL,
        #     trackType='bigBed',
        #     visibility='dense',
        #     thickDrawItem='on',
        #     priority=self.priority,
        # )
        #
        # # Return the BigBed track
        # self.track = Track(
        #     trackFile=myBigBedFilePath,
        #     trackDb=trackDb,
        # )

        print("- Bed %s created" % self.name_bed_generic)
    def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats):

        super(BedSimpleRepeats, self).__init__()

        self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path
        self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
        self.priority = data_bed_simple_repeats["order_index"]

        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")

        # Sort processing
        subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)

        # bedToBigBed processing
        # TODO: Change the name of the bb, to tool + genome + .bb
        trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
        auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as'))
        with open(myBigBedFilePath, 'w') as bigBedFile:
            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name,
                                 typeOption='-type=bed4+12',
                                 autoSql=auto_sql_option)

        # Create the Track Object
        self.createTrack(file_path=trackName,
                         track_name=trackName,
                         long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
                         priority=self.priority,
                         track_file=myBigBedFilePath)

        # dataURL = "tracks/%s" % trackName
        #
        # trackDb = TrackDb(
        #     trackName=trackName,
        #     longLabel=self.name_bed_simple_repeats,
        #     shortLabel=self.getShortName( self.name_bed_simple_repeats ),
        #     trackDataURL=dataURL,
        #     trackType='bigBed 4 +',
        #     visibility='dense',
        #     priority=self.priority,
        # )
        #
        # self.track = Track(
        #     trackFile=myBigBedFilePath,
        #     trackDb=trackDb,
        # )

        print("- Bed simple repeats %s created" % self.name_bed_simple_repeats)
Ejemplo n.º 4
0
    def __init__(self, input_Gff3_false_path, data_gff3):
        super(Gff3, self).__init__()

        self.track = None

        self.input_Gff3_false_path = input_Gff3_false_path
        self.name_gff3 = data_gff3["name"]
        self.priority = data_gff3["order_index"]

        # TODO: See if we need these temporary files as part of the generated files
        genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
        unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")

        # TODO: Refactor into another Class to manage the twoBitInfo and ChromSizes (same process as in Gtf.py)

        # gff3ToGenePred processing
        subtools.gff3ToGenePred(self.input_Gff3_false_path, genePredFile.name)

        # TODO: From there, refactor because common use with Gtf.py
        # genePredToBed processing
        subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)

        # Sort processing
        subtools.sort(unsortedBedFile.name, sortedBedFile.name)

        # TODO: Check if no errors

        # bedToBigBed processing
        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
        trackName = "".join((self.name_gff3, ".bb"))
        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
        with open(myBigBedFilePath, "w") as bigBedFile:
            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)

        # Create the Track Object
        self.createTrack(
            file_path=trackName,
            track_name=trackName,
            long_label=self.name_gff3,
            track_type="bigBed 12 +",
            visibility="dense",
            priority=self.priority,
            track_file=myBigBedFilePath,
        )

        # dataURL = "tracks/%s" % trackName
        #
        # trackDb = TrackDb(
        #     trackName=trackName,
        #     longLabel=self.name_gff3,
        #     shortLabel=self.getShortName( self.name_gff3 ),
        #     trackDataURL=dataURL,
        #     trackType='bigBed 12 +',
        #     visibility='dense',
        #     priority=self.priority,
        # )
        #
        # self.track = Track(
        #     trackFile=myBigBedFilePath,
        #     trackDb=trackDb,
        # )

        print("- Gff3 %s created" % self.name_gff3)