def add_ice_all_partials_arguments(parser): """Add IceAllPartials argument parser.""" parser.add_argument("fastq_filenames", type=str, help="comma delimited fasta files of " + "splitted non-full-length reads") parser.add_argument("ref_fasta", type=str, help="Reference fasta file, most likely " + "ref_consensus.fa from ICE output") parser.add_argument("out_pickle", type=str, help="Output pickle file.") parser.add_argument("--root_dir", dest="root_dir", default="", help="A directory for saving intermediate files.") parser = add_sge_arguments(parser, blasr_nproc=True) parser = add_fofn_arguments(parser, ccs_fofn=True) parser.add_argument("--sa", dest="sa_file", default=None, help="saffix array of ref_fasta") parser.add_argument("--done", dest="done_filename", type=str, help="An empty file generated to indicate that " + "out_pickle is done.") return parser
def add_ice_all_partials_arguments(parser): """Add IceAllPartials argument parser.""" parser.add_argument("fasta_filenames", type=str, help="comma delimited fasta files of " + "splitted non-full-length reads") parser.add_argument("ref_fasta", type=str, help="Reference fasta file, most likely " + "ref_consensus.fa from ICE output") parser.add_argument("out_pickle", type=str, help="Output pickle file.") parser.add_argument("--root_dir", dest="root_dir", default="", help="A directory for saving intermediate files.") parser = add_sge_arguments(parser, blasr_nproc=True) parser = add_fofn_arguments(parser, ccs_fofn=True) parser.add_argument("--sa", dest="sa_file", default=None, help="saffix array of ref_fasta") parser.add_argument("--done", dest="done_filename", type=str, help="An empty file generated to indicate that " + "out_pickle is done.") 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, 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
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
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
def add_ice_quiver_i_arguments(parser): """Add IceQuiverI (ice_quiver.py i) arguments.""" parser = add_cluster_root_dir_as_positional_argument(parser) helpstr = "Call quiver to polish clusters in the (i / N)-th chunk." parser.add_argument("i", help=helpstr, type=int) helpstr = "Divide clusters into N chunks." parser.add_argument("N", help=helpstr, type=int) parser = add_fofn_arguments(parser, bas_fofn=True, fasta_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, fasta_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, fasta_fofn=True) parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True) return parser