def get_argument_parser():
ap = get_default_argparser_with_base_opts(get_version(),
"Toolkit for cDNA analysis.", default_level="WARN")
subparsers = ap.add_subparsers(dest="subCommand")
arg_parser = subparsers.add_parser(
'classify',
description="Classify reads based on whether they are " +
"non-chimeric, full length and have their 5', " +
"3' and poly A tail seen.")
# Add arguments for subcommand classify
add_classify_arguments(_wrap_parser(arg_parser))
arg_parser = subparsers.add_parser(
'cluster',
description='Discover consensus isoforms based on ' +
'quality controlled non-chimeric, ' +
'full length reads to reference genome.')
# Add arguments for subcommand cluster
add_cluster_arguments(_wrap_parser(arg_parser))
arg_parser = subparsers.add_parser(
'subset',
description='Subset annotated reads in FASTA format.')
add_subset_arguments(_wrap_parser(arg_parser))
ap.add_argument(
"--profile", action="store_true",
help="Print runtime profile at exit")
return ap
def _get_parser():
p = get_default_argparser_with_base_opts(description=__doc__,
version=__version__,
default_level="INFO")
p.add_argument("job_id", help="SMRT Link Job ID (or UUID)")
add_smrtlink_server_args(p)
p.add_argument("--retry-on",
action="store",
type=lambda arg: [int(x) for x in arg.split(",")],
default=[],
help="HTTP error codes to retry")
p.add_argument("--json",
action="store",
default=None,
help="Name of output file to write")
p.add_argument("--max-time",
action="store",
type=int,
default=None,
help="Max time to wait before aborting")
p.add_argument(
"--poll-interval",
action="store",
type=int,
default=60,
help=
"Time to sleep between polling for job state. If set to zero, the program will exit immediately after getting job status, regardless of state."
)
return p
def get_argument_parser():
ap = get_default_argparser_with_base_opts(get_version(),
"Toolkit for cDNA analysis.",
default_level="WARN")
subparsers = ap.add_subparsers(dest="subCommand")
arg_parser = subparsers.add_parser(
'classify',
description="Classify reads based on whether they are " +
"non-chimeric, full length and have their 5', " +
"3' and poly A tail seen.")
# Add arguments for subcommand classify
add_classify_arguments(_wrap_parser(arg_parser))
arg_parser = subparsers.add_parser(
'cluster',
description='Discover consensus isoforms based on ' +
'quality controlled non-chimeric, ' +
'full length reads to reference genome.')
# Add arguments for subcommand cluster
add_cluster_arguments(_wrap_parser(arg_parser))
arg_parser = subparsers.add_parser(
'subset', description='Subset annotated reads in FASTA format.')
add_subset_arguments(_wrap_parser(arg_parser))
ap.add_argument("--profile",
action="store_true",
help="Print runtime profile at exit")
return ap
def get_parser():
desc = "Testkit Tool to run pbsmrtpipe jobs."
p = get_default_argparser_with_base_opts(__version__, desc)
funcs = [
TU.add_override_chunked_mode, TU.add_override_distribute_option,
_add_config_file_option, add_tests_only_option,
add_ignore_test_failures_option, add_output_xml_option
]
f = compose(*funcs)
p = f(p)
return p
def get_parser():
desc = "Testkit Tool to run pbsmrtpipe jobs."
p = get_default_argparser_with_base_opts(__version__, desc)
funcs = [TU.add_override_chunked_mode,
TU.add_override_distribute_option,
_add_config_file_option,
add_tests_only_option,
add_ignore_test_failures_option,
add_output_xml_option]
f = compose(*funcs)
p = f(p)
return p
def get_parser():
p = get_default_argparser_with_base_opts(
version=__version__,
description=__doc__)
p.add_argument("dir_name", type=validate_dir)
return p
def get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__)
p.add_argument("dir_name", type=validate_dir)
return p
