comparison BedSpliceJunctions.py @ 26:df42241d3731 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty

25:99dad5f9444c

        self.name_bed_splice_junctions = data_bed_splice_junctions["name"]
        self.priority = data_bed_splice_junctions["order_index"]
        self.track_color = data_bed_splice_junctions["track_color"]
        # TODO: Think about how to avoid repetition of the group_name everywhere
        self.group_name = data_bed_splice_junctions["group_name"]
        if data_bed_splice_junctions["long_label"]:
            self.long_label = data_bed_splice_junctions["long_label"]
        else:
            self.long_label = self.name_bed_splice_junctions
        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")

        with open(myBigBedFilePath, 'w') as bigBedFile:
            subtools.bedToBigBed(sortedBedFile.name,
                                 self.chromSizesFile.name,
                                 bigBedFile.name,
                                 typeOption='bed12+1',
                                 autoSql=auto_sql_option)

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

        # dataURL = "tracks/%s" % trackName
        #
        # trackDb = TrackDb(
        #     trackName=trackName,

26:df42241d3731

        self.name_bed_splice_junctions = data_bed_splice_junctions["name"]
        self.priority = data_bed_splice_junctions["order_index"]
        self.track_color = data_bed_splice_junctions["track_color"]
        # TODO: Think about how to avoid repetition of the group_name everywhere
        self.group_name = data_bed_splice_junctions["group_name"]
        self.database = data_bed_splice_junctions["database"]
        if data_bed_splice_junctions["long_label"]:
            self.long_label = data_bed_splice_junctions["long_label"]
        else:
            self.long_label = self.name_bed_splice_junctions
        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")

        with open(myBigBedFilePath, 'w') as bigBedFile:
            subtools.bedToBigBed(sortedBedFile.name,
                                 self.chromSizesFile.name,
                                 bigBedFile.name,
                                 typeOption='bed12+1',
                                 autoSql=auto_sql_option,
                                 extraIndex='name'
                                 )

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

        # dataURL = "tracks/%s" % trackName
        #
        # trackDb = TrackDb(
        #     trackName=trackName,