#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()
######################################################## #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)
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)
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)
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')