def add_ice_partial_one_arguments(parser): """Add arguments for assigning nfl reads of a given input fasta to unpolished isoforms.""" parser.add_argument("input_fasta", help="Input fasta split file") parser.add_argument("ref_fasta", help="Reference fasta file, most likely " + "ref_consensus.fa from ICE output") parser.add_argument("out_pickle", type=str, help="Output pickle files.") parser = add_fofn_arguments(parser, ccs_fofn=True) parser.add_argument("--sa", dest="sa_file", default=None, help="Suffix 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.") parser.add_argument("--blasr_nproc", dest="blasr_nproc", type=int, default=12, help="blasr -nproc, number of CPUs [default: 12]") parser.add_argument( "--use_finer_qv", action="store_true", default=False, help="Use finer QV which uses more memory & time [default: False]") return parser
def set_parser(parser): """Get 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_options(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") 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_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 set_parser(parser): """Get arguments.""" parser.add_argument("input_fasta", help="Input fasta split file") parser.add_argument("ref_fasta", help="Reference fasta file, most likely " + "ref_consensus.fa from ICE output") parser.add_argument("out_pickle", type=str, default=None, help="Output pickle file.") from pbtools.pbtranscript.PBTranscriptOptions import add_fofn_arguments 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", help="An empty file generated to indicate that" + "out_pickle is done.") parser.add_argument("--blasr_nproc", dest="blasr_nproc", type=int, default=12, help="blasr -nproc, number of CPUs [default: 12]") 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 set_parser(parser): """Set argument parser.""" parser.add_argument("root_dir", type=str, default=None, help="Root directory for ICE, " + \ "e.g., SMRTPortal data/clusterOutDir") parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True) parser = add_sge_options(parser, quiver_nproc=True)
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 set_parser(parser): """Set up argument parser.""" parser.add_argument("root_dir", type=str, default=None, help="Root directory for ICE, " + \ "e.g., SMRTPortal data/clusterOutDir") parser = add_nfl_fa_arguments(parser, positional=True) parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True) parser = add_polished_isoforms_arguments(parser) parser = add_sge_options(parser, quiver_nproc=True)
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", 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) return parser
def set_parser(parser): """Get arguments.""" parser.add_argument("input_fasta", help="Input fasta split file") parser.add_argument("ref_fasta", help="Reference fasta file, most likely " + "ref_consensus.fa from ICE output") parser.add_argument("out_pickle", type=str, default=None, help="Output pickle file.") from pbtools.pbtranscript.PBTranscriptOptions import add_fofn_arguments 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", help="An empty file generated to indicate that" + "out_pickle is done." ) parser.add_argument( "--blasr_nproc", dest="blasr_nproc", type=int, default=12, help="blasr -nproc, number of CPUs [default: 12]" ) return parser
def add_ice_partial_one_arguments(parser): """Add arguments for assigning nfl reads of a given input fasta to unpolished isoforms.""" parser.add_argument("input_fastq", help="Input fastq split file") parser.add_argument("ref_fasta", help="Reference fasta file, most likely " + "ref_consensus.fa from ICE output") parser.add_argument("out_pickle", type=str, help="Output pickle files.") parser = add_fofn_arguments(parser, ccs_fofn=True) parser.add_argument("--done", dest="done_filename", type=str, help="An empty file generated to indicate that " + "out_pickle is done.") parser.add_argument("--use_finer_qv", action="store_true", default=False, help="Use finer QV which uses more memory & time [default: False]") # ToDo: comment OUT BLASR-related arguments; using DALIGNER parser.add_argument("--sa", dest="sa_file", default=None, help="Suffix array of ref_fasta") parser.add_argument("--blasr_nproc", dest="blasr_nproc", type=int, default=12, help="blasr -nproc, number of CPUs [default: 12]") 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