blocks = explogparser.getBlocksFromExpLogJson(env['exp_json'], excludeThumbnail=True)
dirs = ['block_%s' % block['id_str'] for block in blocks]
if not is_composite:
dirs=[]
if args.do_sigproc:
set_result_status('Merge Heatmaps')
exclusionMaskFile = 'exclusionMask_%s.txt' % env.get('chipType','').lower()
sigproc.mergeSigProcResults(
dirs,
env['SIGPROC_RESULTS'],
env['shortRunName'],
exclusionMaskFile)
if args.do_basecalling:
set_result_status('Merge Basecaller Results')
# write composite return code
try:
composite_return_code=96
for subdir in dirs:
blockstatus_return_code_file = os.path.join(subdir,"blockstatus.txt")
if os.path.exists(blockstatus_return_code_file):
number_of_total_blocks = len(blocks_to_process)
dirs = ["block_%s" % block["id_str"] for block in blocks_to_process]
if not is_composite:
dirs = []
if args.do_sigproc:
set_result_status("Merge Heatmaps")
# In 5.4 we apply a mask in the bead find stage but also here to be backward compatible
# with from-basecall reanalyses of 5.2 and older OIA results
exclusionMaskFile = "exclusionMask_%s.txt" % env.get("chipType",
"").lower()
sigproc.mergeSigProcResults(dirs, env["SIGPROC_RESULTS"],
env["shortRunName"], exclusionMaskFile)
"""
# write composite return code, not needed anymore ?
try:
composite_return_code=number_of_total_blocks
for subdir in dirs:
blockstatus_return_code_file = os.path.join(subdir,"blockstatus.txt")
if os.path.exists(blockstatus_return_code_file):
with open(blockstatus_return_code_file, 'r') as f:
text = f.read()
if 'Analysis=0' in text:
composite_return_code-=1
composite_return_code_file = os.path.join(SIGPROC_RESULTS,"analysis_return_code.txt")
printtime("MergeTLStatus %s\tpid %d\tpk file %s started" %
(status, os.getpid(), primary_key_file))
except:
traceback.print_exc()
blocks = explogparser.getBlocksFromExpLogJson(env['exp_json'],
excludeThumbnail=True)
dirs = ['block_%s' % block['id_str'] for block in blocks]
if args.do_sigproc:
set_result_status('Merge Heatmaps')
merged_bead_mask_path = os.path.join(env['SIGPROC_RESULTS'],
'MaskBead.mask')
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'])
number_of_total_blocks = len(blocks_to_process)
dirs = ['block_%s' % block['id_str'] for block in blocks_to_process]
if not is_composite:
dirs = []
if args.do_sigproc:
set_result_status('Merge Heatmaps')
# In 5.4 we apply a mask in the bead find stage but also here to be backward compatible
# with from-basecall reanalyses of 5.2 and older OIA results
exclusionMaskFile = 'exclusionMask_%s.txt' % env.get('chipType', '').lower()
sigproc.mergeSigProcResults(
dirs,
env['SIGPROC_RESULTS'],
env['shortRunName'],
exclusionMaskFile)
'''
# write composite return code, not needed anymore ?
try:
composite_return_code=number_of_total_blocks
for subdir in dirs:
blockstatus_return_code_file = os.path.join(subdir,"blockstatus.txt")
if os.path.exists(blockstatus_return_code_file):
with open(blockstatus_return_code_file, 'r') as f:
text = f.read()
if 'Analysis=0' in text:
env,warn = explogparser.getparameter()
blockprocessing.write_version()
sys.stdout.flush()
sys.stderr.flush()
blocks = explogparser.getBlocksFromExpLogJson(env['exp_json'], excludeThumbnail=True)
dirs = ['block_%s' % block['id_str'] for block in blocks]
if args.do_sigproc:
merged_bead_mask_path = os.path.join(env['SIGPROC_RESULTS'], 'MaskBead.mask')
sigproc.mergeSigProcResults(
dirs,
env['SIGPROC_RESULTS'],
env['shortRunName'])
if args.do_basecalling:
# 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:
blockprocessing.printheader()
env = blockprocessing.getparameter()
blockprocessing.write_version()
sys.stdout.flush()
sys.stderr.flush()
blocks = blockprocessing.getBlocksFromExpLog(env['exp_json'], excludeThumbnail=True)
dirs = ['block_%s' % block['id_str'] for block in blocks]
if args.do_sigproc:
sigproc.mergeSigProcResults(
dirs,
env['pathToRaw'],
env['skipchecksum'],
env['SIGPROC_RESULTS'])
if args.do_basecalling:
QualityPath = os.path.join(env['BASECALLER_RESULTS'], 'quality.summary')
libsff = "%s/%s_%s.sff" % (env['BASECALLER_RESULTS'], env['expName'], env['resultsName'])
tfsff = "%s/%s_%s.tf.sff" % (env['BASECALLER_RESULTS'], env['expName'], env['resultsName'])
merged_bead_mask_path = os.path.join(env['SIGPROC_RESULTS'], 'MaskBead.mask')
basecaller.mergeBasecallerResults(
dirs,
QualityPath,
