def set_parser(parser):
"""Get argument parser."""
parser.add_argument("fasta_filenames",
type=str,
help="comma delimited fasta files of " +
"splitted non-full-length reads")
parser.add_argument("ref_fasta",
type=str,
help="Reference fasta file, most likely " +
"ref_consensus.fa from ICE output")
parser.add_argument("out_pickle",
type=str,
help="Output pickle file.")
parser.add_argument("--root_dir",
dest="root_dir",
default="",
help="A directory for saving intermediate files.")
parser = add_sge_options(parser, blasr_nproc=True)
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--sa",
dest="sa_file",
default=None,
help="saffix array of ref_fasta")
return parser
def set_parser(parser):
"""Set argument parser."""
parser.add_argument("root_dir",
type=str,
default=None,
help="Root directory for ICE, " + \
"e.g., SMRTPortal data/clusterOutDir")
parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
parser = add_sge_options(parser, quiver_nproc=True)
def set_parser(parser):
"""Set argument parser."""
parser.add_argument("root_dir",
type=str,
default=None,
help="Root directory for ICE, " + \
"e.g., SMRTPortal data/clusterOutDir")
parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
parser = add_sge_options(parser, quiver_nproc=True)
def set_parser(parser):
"""Set up argument parser."""
parser.add_argument("root_dir",
type=str,
default=None,
help="Root directory for ICE, " + \
"e.g., SMRTPortal data/clusterOutDir")
parser = add_nfl_fa_arguments(parser, positional=True)
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True)
parser = add_polished_isoforms_arguments(parser)
parser = add_sge_options(parser, quiver_nproc=True)
def set_parser(parser):
"""Set up argument parser."""
parser.add_argument("root_dir",
type=str,
default=None,
help="Root directory for ICE, " + \
"e.g., SMRTPortal data/clusterOutDir")
parser = add_nfl_fa_arguments(parser, positional=True)
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True)
parser = add_polished_isoforms_arguments(parser)
parser = add_sge_options(parser, quiver_nproc=True)
def set_parser(parser):
"""Get argument parser."""
parser.add_argument("fasta_filenames",
type=str,
help="comma delimited fasta files of " +
"splitted non-full-length reads")
parser.add_argument("ref_fasta",
type=str,
help="Reference fasta file, most likely " +
"ref_consensus.fa from ICE output")
parser.add_argument("out_pickle", type=str, help="Output pickle file.")
parser.add_argument("--root_dir",
dest="root_dir",
default="",
help="A directory for saving intermediate files.")
parser = add_sge_options(parser, blasr_nproc=True)
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--sa",
dest="sa_file",
default=None,
help="saffix array of ref_fasta")
return parser
