def get_contract_parser(): p = get_base_contract_parser(Constants, default_level="DEBUG") tcp = p.tool_contract_parser add_fofn_arguments(p.arg_parser.parser, bas_fofn=True, tool_contract_parser=tcp) tcp.add_input_file_type(FileTypes.DS_CONTIG, "consensus_fa", name="Consensus isoforms", description="ContigSet of consensus isoforms") tcp.add_input_file_type(FileTypes.PICKLE, "cluster_pickle", name="Clusters", description="Cluster pickle file") tcp.add_input_file_type( FileTypes.PICKLE, "map_nofl_pickle", name="Pickle file", description="Pickle file for non-full-length read mapping") tcp.add_input_file_type(FileTypes.JSON, "json_in", name="JSON file", description="Sentinel file from ice_quiver task") add_cluster_summary_report_arguments(p) add_ice_post_quiver_hq_lq_arguments(p) return p
def get_contract_parser(): """ Return resolved tool contract. input files: idx 0 - ChunkTasksPickle of ClusterChunkTask objects idx 1 - sentinel txt output files: idx 0 - consensus_isoforms.fa idx 1 - summary.json idx 2 - cluster_report.csv idx 3 - hq_isoforms.contigset.xml idx 4 - hq_isoforms.fq idx 5 - lq_isoforms.contigset.xml idx 6 - lq_isoforms.fq idx 7 - hq_lq_prefix_dict.pickle """ p = get_base_contract_parser(Constants, default_level="DEBUG") p.add_input_file_type(FileTypes.PICKLE, "cluster_chunks_pickle", "Pickle In", "Cluster chunks pickle file") # input 0 p.add_input_file_type(FileTypes.TXT, "cluster_sentinel_in", "Sentinel In", "Setinel file") # input idx 1 # output idx 0, consensus_isoforms.contigset, p.add_output_file_type(FileTypes.DS_CONTIG, "consensus_isoforms", name="Unpolished Consensus Isoforms", description="Output unpolished consensus isoforms", default_name="consensus_isoforms") # output idx 1, summary.json, # output idx 2, cluster_report.csv add_cluster_summary_report_arguments(p) # output idx 3, hq_isoforms_fa, idx 4, hq_isoforms_fq, # idx 5 lq_isoforms_fa, idx 6 lq_isoforms_fq add_ice_post_quiver_hq_lq_arguments(p) # output idx 7, hq_lq_prefix_dict.pickle p.add_output_file_type( FileTypes.PICKLE, "hq_lq_prefix_dict", name="HQ LQ Sample Prefix Dict", description="Pickle mapping HQ (LQ) sample prefixes to ICE dir", default_name="hq_lq_prefix_dict") # user specified sample name. p.add_str(option_id=Constants.SAMPLE_NAME_ID, option_str="sample_name", default=Constants.SAMPLE_NAME_DEFAULT, name="sample Name", description="Sample Name") return p
def get_contract_parser(): """ Return resolved tool contract. input files: idx 0 - ChunkTasksPickle of ClusterChunkTask objects idx 1 - sentinel txt output files: idx 0 - consensus_isoforms.fa idx 1 - summary.json idx 2 - cluster_report.csv idx 3 - hq_isoforms.contigset.xml idx 4 - hq_isoforms.fq idx 5 - lq_isoforms.contigset.xml idx 6 - lq_isoforms.fq idx 7 - hq_lq_prefix_dict.pickle """ p = get_base_contract_parser(Constants, default_level="DEBUG") p.add_input_file_type(FileTypes.PICKLE, "cluster_chunks_pickle", "Pickle In", "Cluster chunks pickle file") # input 0 p.add_input_file_type(FileTypes.TXT, "cluster_sentinel_in", "Sentinel In", "Setinel file") # input idx 1 # output idx 0, consensus_isoforms.contigset, p.add_output_file_type(FileTypes.DS_CONTIG, "consensus_isoforms", name="Unpolished Consensus Isoforms", description="Output unpolished consensus isoforms", default_name="consensus_isoforms") # output idx 1, summary.json, # output idx 2, cluster_report.csv add_cluster_summary_report_arguments(p) # output idx 3, hq_isoforms_fa, idx 4, hq_isoforms_fq, # idx 5 lq_isoforms_fa, idx 6 lq_isoforms_fq add_ice_post_quiver_hq_lq_arguments(p) # output idx 7, hq_lq_prefix_dict.pickle p.add_output_file_type(FileTypes.PICKLE, "hq_lq_prefix_dict", name="HQ LQ Sample Prefix Dict", description="Pickle mapping HQ (LQ) sample prefixes to ICE dir", default_name="hq_lq_prefix_dict") # user specified sample name. p.add_str(option_id=Constants.SAMPLE_NAME_ID, option_str="sample_name", default=Constants.SAMPLE_NAME_DEFAULT, name="sample Name", description="Sample Name") return p
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_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 get_contract_parser(): p = get_base_contract_parser(Constants, default_level="DEBUG") tcp = p.tool_contract_parser add_fofn_arguments(p.arg_parser.parser, bas_fofn=True, tool_contract_parser=tcp) tcp.add_input_file_type(FileTypes.DS_CONTIG, "consensus_fa", name="Consensus isoforms", description="ContigSet of consensus isoforms") tcp.add_input_file_type(FileTypes.PICKLE, "cluster_pickle", name="Clusters", description="Cluster pickle file") tcp.add_input_file_type(FileTypes.PICKLE, "map_nofl_pickle", name="Pickle file", description="Pickle file for non-full-length read mapping") tcp.add_input_file_type(FileTypes.JSON, "json_in", name="JSON file", description="Sentinel file from ice_quiver task") add_cluster_summary_report_arguments(p) add_ice_post_quiver_hq_lq_arguments(p) return p
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_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_quiver_postprocess_arguments(arg_parser): """Add arugments for IceQuiverPostprocess ($ICE_QUIVER_PY postprocess).""" arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser) arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser) tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser)) arg_parser.add_argument("--use_sge", default=False, dest="use_sge", action="store_true", help="quiver jobs have been submitted to sge." "Check qstat") arg_parser.add_argument("--quit_if_not_done", default=False, dest="quit_if_not_done", action="store_true", help="Quit if quiver jobs haven't been completed.") return arg_parser
def add_ice_quiver_postprocess_arguments(arg_parser): """Add arugments for IceQuiverPostprocess ($ICE_QUIVER_PY postprocess).""" arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser) arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser) tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser)) arg_parser.add_argument("--use_sge", default=False, dest="use_sge", action="store_true", help="quiver jobs have been submitted to sge." "Check qstat") arg_parser.add_argument("--quit_if_not_done", default=False, dest="quit_if_not_done", action="store_true", help="Quit if quiver jobs haven't been completed.") return arg_parser