コード例 #1
0
                add_status("MergeBarcodedBasecallerBamsTrimmed", 0)
            except:
                traceback.print_exc()
                add_status("MergeBarcodedBasecallerBamsTrimmed", 1)
            try:
                basecaller.merge_barcoded_basecaller_bams(
                    env['BASECALLER_RESULTS'])
                add_status("MergeBarcodedBasecallerBams", 0)
            except:
                traceback.print_exc()
                add_status("MergeBarcodedBasecallerBams", 1)

        set_result_status('TF Processing')
        try:
            basecaller.tf_processing(
                os.path.join(env['BASECALLER_RESULTS'],
                             "rawtf.basecaller.bam"), env['tfKey'],
                env['flowOrder'], env['BASECALLER_RESULTS'], '.')
            add_status("TF Processing", 0)
        except:
            traceback.print_exc()
            add_status("TF Processing", 1)

        ##################################################
        # Unfiltered BAM
        ##################################################

        if not isProtonBlock:
            try:
                if os.path.exists(
                        os.path.join(env['BASECALLER_RESULTS'],
                                     'unfiltered.untrimmed')):
コード例 #2
0
ファイル: BlockTLScript.py プロジェクト: GerritvanNiekerk/TS
            except:
                traceback.print_exc()
                add_status("MergeBarcodedBasecallerBamsTrimmed", 1)
            try:
                basecaller.merge_barcoded_basecaller_bams(env['BASECALLER_RESULTS'])
                add_status("MergeBarcodedBasecallerBams", 0)
            except:
                traceback.print_exc()
                add_status("MergeBarcodedBasecallerBams", 1)


        set_result_status('TF Processing')
        try:
            basecaller.tf_processing(
                os.path.join(env['BASECALLER_RESULTS'], "rawtf.basecaller.bam"),
                env['tfKey'],
                env['flowOrder'],
                env['BASECALLER_RESULTS'],
                '.')
            add_status("TF Processing", 0)
        except:
            traceback.print_exc()
            add_status("TF Processing", 1)


        ##################################################
        # Unfiltered BAM
        ##################################################

        if not isProtonBlock:
            try:
                if os.path.exists(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.untrimmed')):
コード例 #3
0
ファイル: BlockTLScript.py プロジェクト: golharam/TS
            env['sfftrim_args'],
            env['libraryKey'],
            env['flowOrder'],
            env['barcodeId'],
            env['barcodesplit_filter'],
            env['DIR_BC_FILES'],
            os.path.join("barcodeList.txt"),
            os.path.join(env['SIGPROC_RESULTS'], "bfmask.bin"),
            os.path.join(env['BASECALLER_RESULTS'], "barcodeMask.bin"),
            generate_beadsummary,
            env['BASECALLER_RESULTS'])

        basecaller.tf_processing(
            env['SIGPROC_RESULTS'],
            tfsff_path,
            env['libraryKey'],
            env['tfKey'],
            env['flowOrder'],
            env['BASECALLER_RESULTS'])


        ##################################################
        # Unfiltered SFF
        ##################################################
        top_dir = os.getcwd()
        try:
            unfiltered_dir = "unfiltered"
            if os.path.exists(unfiltered_dir):

                #change to the unfiltered dir
                os.chdir(os.path.join(top_dir,unfiltered_dir))