def main(argv=sys.argv):
mp = get_argument_parser()
return pacbio_args_runner(argv=argv[1:],
parser=mp,
args_runner_func=args_runner,
alog=log,
setup_log_func=setup_log)
def resolved_tool_contract_to_args(resolved_tool_contract):
args = [
"subset",
resolved_tool_contract.task.input_files[0],
resolved_tool_contract.task.output_files[0],
]
return get_argument_parser().parse_args(args)
def resolved_tool_contract_to_args(resolved_tool_contract):
args = [
"subset",
resolved_tool_contract.task.input_files[0],
resolved_tool_contract.task.output_files[0],
]
return get_argument_parser().parse_args(args)
def main(argv=sys.argv):
mp = get_argument_parser()
return pacbio_args_runner(
argv=argv[1:],
parser=mp,
args_runner_func=args_runner,
alog=log,
setup_log_func=setup_log)
def task_to_args(task, ccs_file, nproc, use_finer_qv=False):
"""Convert a ClusterChunkTask to 'pbtranscript cluster' args."""
args = ["--verbose",
"cluster",
"--ccs_fofn", ccs_file,
"--blasr_nproc", str(nproc)]
if use_finer_qv:
args.append("--use_finer_qv")
assert op.exists(task.flnc_file)
args.extend(["-d", task.cluster_out_dir,
task.flnc_file,
task.consensus_isoforms_file])
return get_argument_parser().parse_args(args)
def task_to_args(task, ccs_file, nproc, use_finer_qv=False):
"""Convert a ClusterChunkTask to 'pbtranscript cluster' args."""
args = [
"--verbose", "cluster", "--ccs_fofn", ccs_file, "--blasr_nproc",
str(nproc)
]
if use_finer_qv:
args.append("--use_finer_qv")
assert op.exists(task.flnc_file)
args.extend([
"-d", task.cluster_out_dir, task.flnc_file,
task.consensus_isoforms_file
])
return get_argument_parser().parse_args(args)
def resolved_tool_contract_to_args(resolved_tool_contract):
"""Convert resolved tool contract to args."""
rtc = resolved_tool_contract
args = [
"--verbose",
"classify",
resolved_tool_contract.task.input_files[0],
resolved_tool_contract.task.output_files[0],
"--flnc",
resolved_tool_contract.task.output_files[1],
"--nfl",
resolved_tool_contract.task.output_files[2],
"--summary",
resolved_tool_contract.task.output_files[3], # JSON
"--report",
resolved_tool_contract.task.output_files[4], # CSV
"--min_seq_len",
str(rtc.task.options[Constants.MIN_SEQ_LEN_ID]),
"--cpus",
str(resolved_tool_contract.task.nproc),
"--outDir",
op.dirname(rtc.task.output_files[0]),
"--ignore-empty-output",
]
if rtc.task.options[Constants.IGNORE_POLYA_ID]:
args.append("--ignore_polyA")
primers_str_obj = rtc.task.options[Constants.PRIMER_SEQUENCES_ID]
primers_str = str(primers_str_obj).strip().translate(None, '\'\" ')
if primers_str_obj is not None and primers_str not in ('None', ''):
logging.info("Detected customer primer: %s", primers_str)
# Save primer sequences to a fasta file under output dir
primer_fasta_records = parse_primer_sequences(primers_str=primers_str)
d = op.dirname(resolved_tool_contract.task.output_files[2])
mkdir(d)
primer_fn = op.join(d, "customer_primers.fasta")
with FastaWriter(primer_fn) as writer:
for record in primer_fasta_records:
writer.writeRecord(record)
logging.info("Customer primer sequences written to file %s", primer_fn)
args.append("-p")
args.append("%s" % primer_fn)
else:
logging.info("No customer primer detected.")
return get_argument_parser().parse_args(args)
def resolved_tool_contract_to_args(rtc):
args = [
"--verbose",
"cluster",
"--nfl_fa", rtc.task.input_files[1],
"--ccs_fofn", rtc.task.input_files[2],
"--bas_fofn", rtc.task.input_files[3],
"--blasr_nproc", str(rtc.task.nproc),
"--quiver_nproc", str(rtc.task.nproc),
"--summary", str(rtc.task.output_files[1]), # output 1: JSON
"--report", rtc.task.output_files[2], # output 2: CSV
"--pickle_fn", str(rtc.task.output_files[3]), # output 3: pickle
]
#if rtc.task.options.get(Constants.USE_FINER_QV_ID, False):
# args.append("--use_finer_qv")
args.extend([
"-d", os.path.dirname(rtc.task.output_files[1]),
# NOTE old smrtpipe script has this:
# --unique_id 91373 --cDNA_size under1k
rtc.task.input_files[0],
rtc.task.output_files[0], # output 0: ContigSet
])
log.info("ARGUMENTS: %s" % " ".join(args))
return get_argument_parser().parse_args(args)