def add_ice_partial_one_arguments(parser): """Add arguments for assigning nfl reads of a given input fasta to unpolished isoforms.""" parser.add_input_file_type(FileTypes.DS_CONTIG, "input_fasta", name="ContigSet", description="ContigSet of non-full-length reads") parser.add_input_file_type(FileTypes.DS_CONTIG, "ref_fasta", name="Reference ContigSet", description="Reference fasta file, most likely " + "ref_consensus.fasta from ICE output") arg_parser = add_fofn_arguments(parser.arg_parser.parser, ccs_fofn=True, tool_contract_parser=parser.tool_contract_parser) parser.add_output_file_type(FileTypes.PICKLE, "out_pickle", name="JSON pickle", description="Output pickle file", default_name="ice_partial_one") arg_parser.add_argument("--done", dest="done_filename", type=str, help="An empty file generated to indicate that " + "out_pickle is done.") arg_parser = add_use_blasr_argument(arg_parser) arg_parser = add_tmp_dir_argument(arg_parser) # ToDo: comment OUT BLASR-related arguments; using DALIGNER arg_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_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.fasta 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("--done", dest="done_filename", type=str, help="An empty file generated to indicate that " + "out_pickle is done.") 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_partial_one_arguments(parser): """Add arguments for assigning nfl reads of a given input fasta to unpolished isoforms.""" parser.add_argument("input_fasta", help="Non full-length reads (fasta)") parser.add_argument("--input_fastq", default=None, help="Non full-length reads (fastq). If not given, no QVs are used.") parser.add_argument("ref_fasta", help="Reference fasta, most likely ref.consensus.fasta") parser.add_argument("out_pickle", help="Output pickle file", default="ice_partial_one") parser.add_argument("--done", dest="done_filename", type=str, help="An empty file generated to indicate that " + "out_pickle is done.") parser = add_partial_argument(parser) 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_partial_one_arguments(parser): """Add arguments for assigning nfl reads of a given input fasta to unpolished isoforms.""" parser.add_input_file_type( FileTypes.DS_CONTIG, "input_fasta", name="ContigSet", description="ContigSet of non-full-length reads") parser.add_input_file_type( FileTypes.DS_CONTIG, "ref_fasta", name="Reference ContigSet", description="Reference fasta file, most likely " + "ref_consensus.fasta from ICE output") arg_parser = add_fofn_arguments( parser.arg_parser.parser, ccs_fofn=True, tool_contract_parser=parser.tool_contract_parser) parser.add_output_file_type(FileTypes.PICKLE, "out_pickle", name="JSON pickle", description="Output pickle file", default_name="ice_partial_one") arg_parser.add_argument("--done", dest="done_filename", type=str, help="An empty file generated to indicate that " + "out_pickle is done.") arg_parser = add_use_blasr_argument(arg_parser) arg_parser = add_tmp_dir_argument(arg_parser) # ToDo: comment OUT BLASR-related arguments; using DALIGNER arg_parser.add_argument("--blasr_nproc", dest="blasr_nproc", type=int, default=12, help="blasr --nproc, number of CPUs [default: 12]") return parser