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_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_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_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_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_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 ($ICE_QUIVER_PY postprocess)."""
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser)
tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser))
arg_parser.add_argument("--use_sge",
default=False,
dest="use_sge",
action="store_true",
help="quiver jobs have been submitted to sge."
"Check qstat")
arg_parser.add_argument("--quit_if_not_done",
default=False,
dest="quit_if_not_done",
action="store_true",
help="Quit if quiver jobs haven't been completed.")
return arg_parser
def add_ice_quiver_postprocess_arguments(arg_parser):
"""Add arugments for IceQuiverPostprocess ($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
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
