#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')
