def add_ice_quiver_merge_arguments(parser): """Add IceQuiverMerge arguments.""" parser = add_cluster_root_dir_as_positional_argument(parser) helpstr = "Number of workload chunks." parser.add_argument("N", help=helpstr, type=int) return parser
def add_ice_partial_merge_arguments(parser): """Add IcePartialmerge arguments.""" parser = add_cluster_root_dir_as_positional_argument(parser) helpstr = "Non-full-length reads have been splitted into N chunks." parser.add_argument("N", help=helpstr, type=int) return parser
def add_ice_partial_split_arguments(parser): """Add arguments for ice_partial split.""" parser = add_cluster_root_dir_as_positional_argument(parser) parser = add_nfl_fa_argument(parser, positional=True) helpstr = "Split non-full-length reads into N chunks, N < 100." parser.add_argument("N", help=helpstr, type=int)
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) parser = add_ice_post_quiver_hq_lq_arguments(parser) parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True) parser = add_tmp_dir_argument(parser) return parser
def add_ice_quiver_all_arguments(parser): """Add arguments for IceQuiverAll, including arguments for IceQuiver and IceQuiverPostprocess.""" arg_parser = parser.arg_parser.parser tcp = parser.tool_contract_parser arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser) arg_parser = add_fofn_arguments(arg_parser, bas_fofn=True, tool_contract_parser=parser.tool_contract_parser) tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser)) arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser) arg_parser = add_sge_arguments(arg_parser, quiver_nproc=True, blasr_nproc=True) arg_parser = add_tmp_dir_argument(arg_parser) return parser
def add_ice_quiver_i_arguments(parser): """Add IceQuiverI (ice_quiver.py i) arguments.""" parser = add_cluster_root_dir_as_positional_argument(parser) helpstr = "Divide clusters into N chunks." parser.add_argument("N", help=helpstr, type=int) helpstr = "Call quiver to polish clusters in the (i / N)-th chunk." parser.add_argument("i", nargs="+", help=helpstr, type=int) parser = add_fofn_arguments(parser, bas_fofn=True) parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True) parser = add_tmp_dir_argument(parser) return parser
def add_ice_quiver_all_arguments(parser): """Add arguments for IceQuiverAll, including arguments for IceQuiver and IceQuiverPostprocess.""" arg_parser = parser.arg_parser.parser tcp = parser.tool_contract_parser arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser) arg_parser = add_fofn_arguments( arg_parser, bas_fofn=True, tool_contract_parser=parser.tool_contract_parser) tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser)) arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser) arg_parser = add_sge_arguments(arg_parser, quiver_nproc=True, blasr_nproc=True) arg_parser = add_tmp_dir_argument(arg_parser) return parser
def add_ice_partial_i_arguments(parser): """Add IcePartialI arguments.""" parser = add_cluster_root_dir_as_positional_argument(parser) helpstr = "To process the i-th chunk of non-full-length reads." parser.add_argument("i", nargs="+", help=helpstr, type=int) parser.add_argument("--blasr_nproc", type=int, dest="blasr_nproc", action="store", default=12, help="Number of cores for each BLASR job.") parser = add_fofn_arguments(parser, ccs_fofn=True) parser = add_tmp_dir_argument(parser) return parser
def add_ice_quiver_postprocess_arguments(arg_parser): """Add arugments for IceQuiverPostprocess ($ICE_QUIVER_PY postprocess).""" arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser) arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser) tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser)) arg_parser.add_argument("--use_sge", default=False, dest="use_sge", action="store_true", help="quiver jobs have been submitted to sge." "Check qstat") arg_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 arg_parser
def add_ice_quiver_arguments(parser): """Add arguments for IceQuiver, not including IceQuiverPostprocess.""" parser = add_cluster_root_dir_as_positional_argument(parser) parser = add_fofn_arguments(parser, bas_fofn=True) parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True) return parser