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 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)