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)
parser = add_nfl_fq_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)
parser = add_nfl_fq_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_arrow_all_arguments(parser):
arg_parser = parser #parser.arg_parser.parser
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_fofn_arguments(arg_parser, subread_xml=True)
arg_parser = add_cluster_summary_report_arguments(arg_parser)
arg_parser = add_ice_post_arrow_hq_lq_arguments2(arg_parser)
arg_parser = add_sge_arguments(arg_parser, blasr_nproc=True, arrow_nproc=True)
arg_parser = add_tmp_dir_argument(arg_parser)
return arg_parser
def add_ice_arrow_all_arguments(parser):
arg_parser = parser #parser.arg_parser.parser
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_fofn_arguments(arg_parser, subread_xml=True)
arg_parser = add_cluster_summary_report_arguments(arg_parser)
arg_parser = add_ice_post_arrow_hq_lq_arguments2(arg_parser)
arg_parser = add_sge_arguments(arg_parser,
blasr_nproc=True,
arrow_nproc=True)
arg_parser = add_tmp_dir_argument(arg_parser)
return arg_parser
def add_ice_arrow_postprocess_arguments(arg_parser):
"""
Add arguments for IceArrowPostProcess2 ($ICE_ARROW_PY postprocess).
"""
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_ice_post_arrow_hq_lq_arguments2(arg_parser)
arg_parser = add_cluster_summary_report_arguments(arg_parser)
arg_parser.add_argument("--quit_if_not_done",
default=False,
dest="quit_if_not_done",
action="store_true",
help="Quit if arrow jobs haven't been completed.")
return arg_parser
def add_ice_arrow_postprocess_arguments(arg_parser):
"""
Add arguments for IceArrowPostProcess2 ($ICE_ARROW_PY postprocess).
"""
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_ice_post_arrow_hq_lq_arguments2(arg_parser)
arg_parser = add_cluster_summary_report_arguments(arg_parser)
arg_parser.add_argument("--quit_if_not_done",
default=False,
dest="quit_if_not_done",
action="store_true",
help="Quit if arrow jobs haven't been completed.")
return arg_parser
def add_ice_arrow_arguments(parser):
"""Add arguments for IceArrow2, not including IceArrowPostprocess2."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_fofn_arguments(parser, subread_xml=True)
parser = add_sge_arguments(parser, arrow_nproc=True, blasr_nproc=True)
return parser
is_FL=True,
qv_prob_threshold=0.03,
output_pickle_file=None,
tmp_dir=None)
icec.run()
if __name__ == "__main__":
from argparse import ArgumentParser
parser = ArgumentParser("run IceIterative2.")
parser.add_argument("fasta_filenames")
parser.add_argument("fastq_filenames")
parser.add_argument("all_fasta_filename")
parser = add_cluster_root_dir_as_positional_argument(parser)
parser.add_argument("--init_uc_pickle",
default=None,
type=str,
help="Init2 pickle (ex: init.uc.pickle)")
parser = add_ice_arguments(parser)
parser = add_sge_arguments(parser,
blasr_nproc=True,
gcon_nproc=True,
arrow_nproc=False)
args = parser.parse_args()
# currently, the user is NOT allowed to set the definition for full missed start/end
# (i.e. how much of the query must be mapped to consider it a hit)
is_FL=True,
qv_prob_threshold=0.03,
output_pickle_file=None,
tmp_dir=None)
icec.run()
if __name__ == "__main__":
from argparse import ArgumentParser
parser = ArgumentParser("run IceIterative2.")
parser.add_argument("fasta_filenames")
parser.add_argument("fastq_filenames")
parser.add_argument("all_fasta_filename")
parser = add_cluster_root_dir_as_positional_argument(parser)
parser.add_argument("--init_uc_pickle", default=None, type=str, help="Init2 pickle (ex: init.uc.pickle)")
parser = add_ice_arguments(parser)
parser = add_sge_arguments(parser, blasr_nproc=True, gcon_nproc=True, arrow_nproc=False)
args = parser.parse_args()
# currently, the user is NOT allowed to set the definition for full missed start/end
# (i.e. how much of the query must be mapped to consider it a hit)
ice_opts = IceOptions2(ece_penalty=args.ece_penalty,
ece_min_len=args.ece_min_len,
max_missed_start=args.max_missed_start,
max_missed_end=args.max_missed_end,
full_missed_start=30,