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,