def GetBlocksToAnalyze(env):
blocks = []
if is_thumbnail or is_wholechip:
block = {"id_str": "", "datasubdir": "", "jobcmd": [], "jobid": None, "status": None}
base_args = env["analysisArgs"].strip().split(" ")
base_args.append("--libraryKey=%s" % env["libraryKey"])
base_args.append("--tfKey=%s" % env["tfKey"])
base_args.append("--no-subdir --wellsfileonly")
if is_thumbnail:
thumbnailsize = blockprocessing.getThumbnailSize(env["exp_json"])
block["id_str"] = "thumbnail"
base_args.append("--cfiedr-regions-size=50x50")
base_args.append("--block-size=%sx%s" % (thumbnailsize[0], thumbnailsize[1]))
base_args.append("--beadfind-thumbnail 1")
base_args.append("--bkg-debug-param 1")
elif is_wholechip:
block["id_str"] = "wholechip"
base_args.append("--output-dir=%s" % env["SIGPROC_RESULTS"])
block["jobcmd"] = base_args
print base_args
print block
blocks.append(block)
else:
explogblocks = blockprocessing.getBlocksFromExpLog(env["exp_json"])
for block in explogblocks:
# ignore thumbnail
if block["id_str"] == "thumbnail":
continue
base_args = env["analysisArgs"].strip().split(" ")
# raw data dir is last element in analysisArgs and needs the block subdirectory appended
base_args[-1] = os.path.join(base_args[-1], block["datasubdir"])
rawDirectory = base_args[-1]
base_args.append("--libraryKey=%s" % env["libraryKey"])
base_args.append("--no-subdir --wellsfileonly")
base_args.append("--output-dir=%s" % env["SIGPROC_RESULTS"])
block["jobcmd"] = base_args
print "expblock: " + str(block)
if (block["autoanalyze"] and block["analyzeearly"]) or os.path.isdir(rawDirectory):
print "base_args: " + str(base_args)
print "block: " + str(block)
blocks.append(block)
return blocks
if args.verbose:
print "MergeTLScript:",args
if not args.do_sigproc and not args.do_basecalling and not args.do_alignment and not args.do_zipping:
parser.print_help()
sys.exit(1)
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:
