def build_parser(subparsers):
parser = subparsers.add_parser("pyronoise", help="Run PyroNoise",
parents=[run.base_parser()])
pnoise_opts = parser.add_argument_group("PyroNoise Options")
pnoise_opts.add_argument('-s', '--sigma', type=float,
default=60.0, help="""Initial cluster size (see Quince et al)
[default: %(default)s]""")
pnoise_opts.add_argument('-c', '--cutoff', type=float,
default=0.01, help="""Initial cutoff (see Quince et al) [default:
%(default)s]""")
pnoise_opts.add_argument('-rin', '--lookup-file',
help="""Lookup file""")
parser.add_argument('sff_file', help="""SFF file""")
parser.add_argument('-v', '--verbose', default=logging.INFO,
action="store_const", const=logging.DEBUG)
clean_group = parser.add_argument_group("Cleaning parameters")
clean_group.add_argument('--min-flows', default=320, type=int,
help="""Minimum flow count [default: %(default)s]""")
clean_group.add_argument('--max-flows', default=720, type=int,
help="""Maximum flow count [default: %(default)s]""")
clean_group.add_argument('--max-empty', default=0, type=int,
help="""Maximum empty flowgrams to accept before truncation
[default: %(default)s]""")
clean_group.add_argument('--primer', default='.',
help="Primer used", type=util.ambiguous_pattern)
return parser
def build_parser(subparsers):
parser = subparsers.add_parser("seqnoise",
help="Run SeqNoise",
parents=[run.base_parser()])
snoise_opts = parser.add_argument_group("SeqNoise Options")
snoise_opts.add_argument('-s',
'--sigma',
type=float,
default=30.0,
help="""Sigma (see Quince et al)
[default: %(default)s]""")
snoise_opts.add_argument(
'-c',
'--cutoff',
type=float,
default=0.08,
help="""Initial cutoff (see Quince et al) [default:
%(default)s]""")
snoise_opts.add_argument('-rin', '--lookup-file', help="""Lookup file""")
parser.add_argument('-v',
'--verbose',
default=logging.INFO,
action="store_const",
const=logging.DEBUG)
parser.add_argument('fasta_file', help="""PyroNoised fasta file""")
parser.add_argument('mapping_file', help="""PyroNoise .mapping file""")
return parser
def build_parser(subparsers):
parser = subparsers.add_parser("pyronoise",
help="Run PyroNoise",
parents=[run.base_parser()])
pnoise_opts = parser.add_argument_group("PyroNoise Options")
pnoise_opts.add_argument('-s',
'--sigma',
type=float,
default=60.0,
help="""Initial cluster size (see Quince et al)
[default: %(default)s]""")
pnoise_opts.add_argument(
'-c',
'--cutoff',
type=float,
default=0.01,
help="""Initial cutoff (see Quince et al) [default:
%(default)s]""")
pnoise_opts.add_argument('-rin', '--lookup-file', help="""Lookup file""")
parser.add_argument('sff_file', help="""SFF file""")
parser.add_argument('-v',
'--verbose',
default=logging.INFO,
action="store_const",
const=logging.DEBUG)
clean_group = parser.add_argument_group("Cleaning parameters")
clean_group.add_argument(
'--min-flows',
default=320,
type=int,
help="""Minimum flow count [default: %(default)s]""")
clean_group.add_argument(
'--max-flows',
default=720,
type=int,
help="""Maximum flow count [default: %(default)s]""")
clean_group.add_argument(
'--max-empty',
default=0,
type=int,
help="""Maximum empty flowgrams to accept before truncation
[default: %(default)s]""")
clean_group.add_argument('--primer',
default='.',
help="Primer used",
type=util.ambiguous_pattern)
return parser
def build_parser(subparsers):
parser = subparsers.add_parser("seqnoise", help="Run SeqNoise",
parents=[run.base_parser()])
snoise_opts = parser.add_argument_group("SeqNoise Options")
snoise_opts.add_argument('-s', '--sigma', type=float,
default=30.0, help="""Sigma (see Quince et al)
[default: %(default)s]""")
snoise_opts.add_argument('-c', '--cutoff', type=float,
default=0.08, help="""Initial cutoff (see Quince et al) [default:
%(default)s]""")
snoise_opts.add_argument('-rin', '--lookup-file',
help="""Lookup file""")
parser.add_argument('-v', '--verbose', default=logging.INFO,
action="store_const", const=logging.DEBUG)
parser.add_argument('fasta_file', help="""PyroNoised fasta file""")
parser.add_argument('mapping_file', help="""PyroNoise .mapping file""")
return parser
