Ejemplo n.º 1
0
        #Make Bead Density Plots                               #
        ########################################################
        bfmaskPath = os.path.join(env['SIGPROC_RESULTS'], "bfmask.bin")
        bfmaskstatspath = os.path.join(env['SIGPROC_RESULTS'], "bfmask.stats")
        try:
            upload_analysismetrics(bfmaskstatspath)
            update_bfmask_artifacts(bfmaskPath,
                                    bfmaskstatspath,
                                    "./",
                                    plot_title=env['shortRunName'])
        except:
            traceback.print_exc()

        set_result_status('Signal Processing')
        status = sigproc.sigproc(env['analysisArgs'], env['libraryKey'],
                                 env['tfKey'], env['pathToRaw'],
                                 env['SIGPROC_RESULTS'])
        add_status("Analysis", status)

        # write return code into file
        try:
            f = open(
                os.path.join(env['SIGPROC_RESULTS'],
                             "analysis_return_code.txt"), 'w')
            f.write(str(status))
            f.close()
            os.chmod(
                os.path.join(env['SIGPROC_RESULTS'],
                             "analysis_return_code.txt"), 0775)
        except:
            traceback.print_exc()
Ejemplo n.º 2
0
        ########################################################
        #Make Bead Density Plots                               #
        ########################################################
        bfmaskPath = os.path.join(env['SIGPROC_RESULTS'],"bfmask.bin")
        bfmaskstatspath = os.path.join(env['SIGPROC_RESULTS'],"bfmask.stats")
        try:
            upload_analysismetrics(bfmaskstatspath)
            update_bfmask_artifacts(bfmaskPath, bfmaskstatspath, "./", plot_title=env['shortRunName'])
        except:
            traceback.print_exc()

        set_result_status('Signal Processing')
        status = sigproc.sigproc(
                    env['analysisArgs'],
                    env['libraryKey'],
                    env['tfKey'],
                    env['pathToRaw'],
                    env['SIGPROC_RESULTS'])
        add_status("Analysis", status)

        # write return code into file
        try:
            f = open(os.path.join(env['SIGPROC_RESULTS'],"analysis_return_code.txt"), 'w')
            f.write(str(status))
            f.close()
            os.chmod(os.path.join(env['SIGPROC_RESULTS'],"analysis_return_code.txt"), 0775)
        except:
            traceback.print_exc()

        if status != 0:
            printtime("ERROR: Analysis finished with status '%s'" % status)
Ejemplo n.º 3
0
        f.write('basecalling = grey\n')
        f.write('sffread = grey\n')
        f.write('alignment = grey')
        f.close()

        if env['doThumbnail']:
            analysisArgs = env['thumbnailAnalysisArgs']
            oninstrumentanalysis = False
        else:
            analysisArgs = env['analysisArgs']
            oninstrumentanalysis = env['oninstranalysis']

        sigproc.sigproc(
            analysisArgs,
            env['libraryKey'],
            env['tfKey'],
            env['pathToRaw'],
            env['SIGPROC_RESULTS'],
            env['shortRunName'],
            oninstrumentanalysis)

    # In case of from-wells or from-basecaller reanalysis of a legacy report, some adjustments may be needed
    handle_legacy_report.handle_sigproc(env['SIGPROC_RESULTS'])

    if args.do_basecalling:

        #make sure pre-conditions for basecaller step are met
        if not os.path.exists(os.path.join(env['SIGPROC_RESULTS'],'1.wells')):
            printtime ("ERROR: missing %s" % os.path.join(env['SIGPROC_RESULTS'],'1.wells') )
            printtime ("ERROR: basecaller pre-conditions not met")
            sys.exit(1)
Ejemplo n.º 4
0
        bfmaskPath = os.path.join(env["SIGPROC_RESULTS"], "bfmask.bin")
        bfmaskstatspath = os.path.join(env["SIGPROC_RESULTS"], "bfmask.stats")
        try:
            upload_analysismetrics(bfmaskstatspath)
            update_bfmask_artifacts(bfmaskPath,
                                    bfmaskstatspath,
                                    "./",
                                    plot_title=env["shortRunName"])
        except Exception:
            traceback.print_exc()

        set_result_status("Signal Processing")
        status = sigproc.sigproc(
            env["analysisArgs"],
            env["libraryKey"],
            env["tfKey"],
            env["pathToRaw"],
            env["SIGPROC_RESULTS"],
        )
        add_status("Analysis", status)

        # write return code into file
        try:
            f = open(
                os.path.join(env["SIGPROC_RESULTS"],
                             "analysis_return_code.txt"), "w")
            f.write(str(status))
            f.close()
            os.chmod(
                os.path.join(env["SIGPROC_RESULTS"],
                             "analysis_return_code.txt"), 0o0775)
Ejemplo n.º 5
0
    libsff_path = os.path.join(env['BASECALLER_RESULTS'], "rawlib.sff")
    tfsff_path = os.path.join(env['BASECALLER_RESULTS'], "rawtf.sff")

    if args.do_sigproc:

        # create analysis progress bar file
        f = open('progress.txt','w')
        f.write('wellfinding = yellow\n')
        f.write('signalprocessing = grey\n')
        f.write('basecalling = grey\n')
        f.write('sffread = grey\n')
        f.write('alignment = grey')
        f.close()

        sigproc.sigproc(
            env['analysisArgs'],
            env['pathToRaw'],
            env['SIGPROC_RESULTS'])


    if args.do_basecalling:

        #make sure pre-conditions for basecaller step are met
        if not os.path.exists(os.path.join(env['SIGPROC_RESULTS'],'1.wells')):
            printtime ("ERROR: basecaller pre-conditions not met")
            sys.exit(1)

        # create analysis progress bar file
        f = open('progress.txt','w')
        f.write('wellfinding = green\n')
        f.write('signalprocessing = green\n')
        f.write('basecalling = yellow\n')