コード例 #1
0
ファイル: MergeTLScript.py プロジェクト: vswilliamson/TS
        if do_composite_alignment or not is_composite:

            set_result_status('Alignment')

            do_ionstats = True
            do_indexing = True

            try:
                alignment.process_datasets(
                    dirs,
                    env['alignmentArgs'],
                    env['ionstatsArgs'],
                    env['BASECALLER_RESULTS'],
                    basecaller_meta_information,
                    env['libraryKey'],
                    graph_max_x,
                    basecaller_datasets,
                    env['ALIGNMENT_RESULTS'],
                    env['realign'],
                    do_ionstats,
                    env['mark_duplicates'],
                    do_indexing,
                    env['barcodeInfo'])
#                add_status("Alignment", 0)
            except:
                traceback.print_exc()
#                add_status("Alignment", 1)

        else: # is_composite and not do_composite_alignment:

            set_result_status('Merge Bam Files')
コード例 #2
0
ファイル: MergeTLScript.py プロジェクト: tw7649116/TS
            basecaller_meta_information = None

        if reference_selected:
            set_result_status('Alignment')

        do_ionstats = True
        do_indexing = True

        alignment.process_datasets(
            dirs,
            env['alignmentArgs'],
            env['ionstatsArgs'],
            env['BASECALLER_RESULTS'],
            basecaller_meta_information,
            env['libraryKey'],
            graph_max_x,
            basecaller_datasets,
            env['ALIGNMENT_RESULTS'],
            env['realign'],
            do_ionstats,
            env['mark_duplicates'],
            do_indexing,
            env['barcodeInfo'])

        '''

    ### OLD per block processing
    if args.do_alignment:

        try:
            c = open(os.path.join(env['BASECALLER_RESULTS'], "BaseCaller.json"),'r')
コード例 #3
0
            basecaller_meta_information = None

        if reference_selected:
            set_result_status("Alignment")

        do_ionstats = True
        do_indexing = True

        alignment.process_datasets(
            dirs,
            env["alignmentArgs"],
            env["ionstatsArgs"],
            env["BASECALLER_RESULTS"],
            basecaller_meta_information,
            env["libraryKey"],
            graph_max_x,
            basecaller_datasets,
            env["ALIGNMENT_RESULTS"],
            env["realign"],
            do_ionstats,
            env["mark_duplicates"],
            do_indexing,
            env["barcodeInfo"],
        )
        """

    ### OLD per block processing
    if args.do_alignment:

        try:
            c = open(os.path.join(env['BASECALLER_RESULTS'], "BaseCaller.json"),'r')
            basecaller_meta_information = json.load(c)
コード例 #4
0
ファイル: BlockTLScript.py プロジェクト: vswilliamson/TS
            do_indexing=False
            do_ionstats=True
        else:
            do_indexing=True
            do_ionstats=True

        try:
            blocks=[]
            alignment.process_datasets(
                blocks,
                env['alignmentArgs'],
                env['ionstatsArgs'],
                env['BASECALLER_RESULTS'],
                basecaller_meta_information if do_ionstats_spatial_accounting else None,
                env['libraryKey'],
                graph_max_x,
                basecaller_datasets,
                env['ALIGNMENT_RESULTS'],
                env['realign'],
                do_ionstats,
                env['mark_duplicates'],
                do_indexing,
                env['barcodeInfo'])
            add_status("Alignment", 0)
        except:
            traceback.print_exc()
            add_status("Alignment", 1)
            printtime ("ERROR: Alignment failed")
            sys.exit(1)