Python add_polished_isoforms_arguments Examples

Example #1

File: Polish.py Project: gonzalezibeas/cDNA_primer

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)

Example #2

File: Polish.py Project: avrajit/cDNA_primer

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)

Example #3

File: IcePostQuiver.py Project: WenchaoLin/cDNA_primer

def set_parser(parser):
    """Set argument parser."""
    parser.add_argument("root_dir", type=str, help="Root directory for ICE, " + "e.g., SMRTPortal data/clusterOutDir")
    parser = add_polished_isoforms_arguments(parser)
    parser.add_argument(
        "--use_sge",
        default=False,
        dest="use_sge",
        action="store_true",
        help="quiver jobs have been submitted to sge." "Check qstat",
    )
    parser.add_argument(
        "--quit_if_not_done",
        default=False,
        dest="quit_if_not_done",
        action="store_true",
        help="Quit if quiver jobs haven't been completed.",
    )

Example #4

File: IcePostQuiver.py Project: wangyuu/cDNA_primer

def set_parser(parser):
    """Set argument parser."""
    parser.add_argument("root_dir",
                        type=str,
                        help="Root directory for ICE, " + \
                             "e.g., SMRTPortal data/clusterOutDir")
    parser = add_polished_isoforms_arguments(parser)
    parser.add_argument("--use_sge",
                        default=False,
                        dest="use_sge",
                        action="store_true",
                        help="quiver jobs have been submitted to sge."
                        "Check qstat")
    parser.add_argument("--quit_if_not_done",
                        default=False,
                        dest="quit_if_not_done",
                        action="store_true",
                        help="Quit if quiver jobs haven't been completed.")