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