Python add_ice_post_quiver_hq_lq_argumentsの例

コード例 #1

ファイル: Polish.py プロジェクト: wangyuu/cDNA_primer

def add_ice_polish_arguments(parser):
    """Set up argument parser."""
    parser = add_cluster_root_dir_as_positional_argument(parser)
    parser = add_nfl_fa_argument(parser, positional=True)
    parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True, fasta_fofn=True)
    parser = add_ice_post_quiver_hq_lq_arguments(parser)
    parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True, sge_env_name=True, sge_queue=True)
    return parser

コード例 #2

def add_ice_quiver_all_arguments(parser):
    """Add arguments for IceQuiverAll, including arguments for IceQuiver and
    IceQuiverPostprocess."""
    parser = add_cluster_root_dir_as_positional_argument(parser)
    parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
    parser = add_cluster_summary_report_arguments(parser)
    parser = add_ice_post_quiver_hq_lq_arguments(parser)
    parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
    return parser

コード例 #3

ファイル: IceQuiverAll.py プロジェクト: 52teth/cDNA_primer

def add_ice_quiver_all_arguments(parser):
    """Add arguments for IceQuiverAll, including arguments for IceQuiver and
    IceQuiverPostprocess."""
    parser = add_cluster_root_dir_as_positional_argument(parser)
    parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
    parser = add_cluster_summary_report_arguments(parser)
    parser = add_ice_post_quiver_hq_lq_arguments(parser)
    parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
    return parser

コード例 #4

ファイル: IceQuiverPostprocess.py プロジェクト: ksahlin/cDNA_primer

def add_ice_quiver_postprocess_arguments(parser):
    """Add arugments for IceQuiverPostprocess (ice_quiver.py postprocess)."""
    parser = add_cluster_root_dir_as_positional_argument(parser)
    parser = add_ice_post_quiver_hq_lq_arguments(parser)
    parser = add_cluster_summary_report_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.")
    return parser

コード例 #5

ファイル: IceQuiverPostprocess.py プロジェクト: yimsea/cDNA_primer

def add_ice_quiver_postprocess_arguments(parser):
    """Add arugments for IceQuiverPostprocess (ice_quiver.py postprocess)."""
    parser = add_cluster_root_dir_as_positional_argument(parser)
    parser = add_ice_post_quiver_hq_lq_arguments(parser)
    parser = add_cluster_summary_report_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.")
    return parser