sigproc.mergeSigProcResults(dirs, env['SIGPROC_RESULTS'],
env['shortRunName'])
if args.do_basecalling:
set_result_status('Merge Basecaller Results')
try:
sigproc.mergeRawPeakSignals(dirs)
except:
traceback.print_exc()
try:
# Only merge metrics and generate plots
basecaller.merge_basecaller_stats(dirs, env['BASECALLER_RESULTS'],
env['SIGPROC_RESULTS'],
env['flows'], env['flowOrder'])
## Generate BaseCaller's composite "Big Data": unmapped.bam. Totally optional
if env.get('libraryName', '') == 'none':
actually_merge_unmapped_bams = True
else:
actually_merge_unmapped_bams = False
if actually_merge_unmapped_bams:
basecaller.merge_basecaller_bam(dirs,
env['BASECALLER_RESULTS'])
except:
traceback.print_exc()
printtime("ERROR: Merge Basecaller Results failed")
if args.do_alignment and env[
'libraryName'] and env['libraryName'] != 'none':
env['tfKey'], 'Test Fragment Beads')
except:
printtime(
"Warning: mergeAvgNukeTraces '%s' 'Test Fragment Beads' failed"
% env['tfKey'])
try:
sigproc.generate_raw_data_traces(env['libraryKey'], env['tfKey'],
env['flowOrder'],
env['SIGPROC_RESULTS'])
except:
traceback.print_exc()
try:
# Only merge standard json files
basecaller.merge_basecaller_stats(dirs, env['BASECALLER_RESULTS'])
except:
traceback.print_exc()
printtime("ERROR: Merge Basecaller Results failed")
try:
c = open(
os.path.join(env['BASECALLER_RESULTS'], "BaseCaller.json"),
'r')
basecaller_meta_information = json.load(c)
c.close()
except:
traceback.print_exc()
raise
basecaller_datasets = blockprocessing.get_datasets_basecaller(
printtime("Warning: mergeAvgNukeTraces '%s' 'Test Fragment Beads' failed" % env['tfKey'])
try:
sigproc.generate_raw_data_traces(
env['libraryKey'],
env['tfKey'],
env['flowOrder'],
env['SIGPROC_RESULTS'])
except:
traceback.print_exc()
try:
# Only merge metrics and generate plots
basecaller.merge_basecaller_stats(
dirs,
env['BASECALLER_RESULTS'],
env['SIGPROC_RESULTS'],
env['flows'],
env['flowOrder'])
RECALIBRATION_RESULTS = os.path.join(env['BASECALLER_RESULTS'],"recalibration")
if not os.path.isdir(RECALIBRATION_RESULTS):
os.makedirs(RECALIBRATION_RESULTS)
cmd = "calibrate --hpmodelMerge"
printtime("DEBUG: Calling '%s':" % cmd)
ret = subprocess.call(cmd,shell=True)
## Generate BaseCaller's composite "Big Data": unmapped.bam. Totally optional
if env.get('libraryName','') == 'none':
actually_merge_unmapped_bams = True
else:
actually_merge_unmapped_bams = False
if actually_merge_unmapped_bams:
basecaller.merge_basecaller_bam(
except:
printtime("Warning: mergeAvgNukeTraces '%s' 'Test Fragment Beads' failed" % env['tfKey'])
try:
sigproc.generate_raw_data_traces(
env['libraryKey'],
env['tfKey'],
env['flowOrder'],
env['SIGPROC_RESULTS'])
except:
traceback.print_exc()
try:
# Only merge standard json files
basecaller.merge_basecaller_stats(
dirs,
env['BASECALLER_RESULTS'])
except:
traceback.print_exc()
printtime("ERROR: Merge Basecaller Results failed")
try:
c = open(os.path.join(env['BASECALLER_RESULTS'], "BaseCaller.json"),'r')
basecaller_meta_information = json.load(c)
c.close()
except:
traceback.print_exc()
raise
basecaller_datasets = blockprocessing.get_datasets_basecaller(env['BASECALLER_RESULTS'])
