kkonganti@0: """Entry script"""
kkonganti@0: 
kkonganti@20: __version__ = "1.1.0"
kkonganti@0: import argparse, datetime, json, logging, os, pandas, sys
kkonganti@0: import lexmapr.pipeline, lexmapr.run_summary
kkonganti@0: from lexmapr.definitions import arg_bins
kkonganti@0: 
kkonganti@0: 
kkonganti@0: def valid_input(file_path):
kkonganti@20:     """Exits if input file is invalid"""
kkonganti@0:     _, file_ext = os.path.splitext(file_path)
kkonganti@20:     if file_ext.lower() != ".csv" and file_ext.lower() != ".tsv":
kkonganti@20:         sys.exit("Please supply a CSV or TSV input file with the correct file extension")
kkonganti@0:     if not os.path.exists(file_path):
kkonganti@20:         sys.exit(f'Input file named "{file_path}" not found')
kkonganti@20:     return file_path.strip()
kkonganti@20: 
kkonganti@0: 
kkonganti@0: def valid_json(file_path):
kkonganti@20:     """Outputs read JSON file and exits if file is invalid"""
kkonganti@0:     try:
kkonganti@20:         with open(file_path, "r") as JSON_file:
kkonganti@0:             try:
kkonganti@20:                 return json.load(JSON_file)
kkonganti@20:             except (json.decoder.JSONDecodeError):
kkonganti@20:                 sys.exit(f"User-defined bins not in readable JSON format")
kkonganti@20:     except (FileNotFoundError):
kkonganti@20:         sys.exit(f'File named "{file_path}" not found')
kkonganti@20: 
kkonganti@0: 
kkonganti@0: def valid_list(list_str):
kkonganti@20:     """Return list of user-defined ontologies"""
kkonganti@20:     return [x.strip().upper() for x in list_str.split(",")]
kkonganti@20: 
kkonganti@0: 
kkonganti@0: if __name__ == "__main__":
kkonganti@0:     # Parse arguments, initiate log file and start run
kkonganti@0:     arg_parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter)
kkonganti@20:     arg_parser.add_argument("input", help="input CSV or TSV file; required", type=valid_input)
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-o", "--output", metavar="\b", help="    output TSV file path; default is stdout"
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-a", "--no_ancestors", action="store_true", help="remove ancestral terms from output"
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-b", "--bin", action="store_true", help="classify samples into default bins"
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-e",
kkonganti@20:         "--embl_ontol",
kkonganti@20:         metavar="\b",
kkonganti@20:         type=valid_list,
kkonganti@20:         help="    user-defined comma-separated ontology short names",
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument("-f", "--full", action="store_true", help="full output format")
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-g", "--graph", action="store_true", help="visualize summaries of mapping and binning"
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-j",
kkonganti@20:         "--graph_only",
kkonganti@20:         action="store_true",
kkonganti@20:         help="only perform visualization with LexMapr output",
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-r", "--remake_cache", action="store_true", help="remake cached resources"
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-u",
kkonganti@20:         "--user_bin",
kkonganti@20:         metavar="\b",
kkonganti@20:         type=valid_json,
kkonganti@20:         help="    path to JSON file with user-defined bins",
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-w",
kkonganti@20:         "--num_words",
kkonganti@20:         metavar="\b",
kkonganti@20:         default=3,
kkonganti@20:         help="    number of word combinations to sample",
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument(
kkonganti@20:         "-p",
kkonganti@20:         "--cpus",
kkonganti@20:         metavar="\b",
kkonganti@20:         default=8,
kkonganti@20:         help="    number of CPUs to try and parallelize permuations on",
kkonganti@20:     )
kkonganti@20:     arg_parser.add_argument("-v", "--version", action="version", version="%(prog)s " + __version__)
kkonganti@0: 
kkonganti@0:     # TODO: encoding argument addded to logging.basicConfig in Python 3.9; now defaults to open()
kkonganti@0:     run_args = arg_parser.parse_args()
kkonganti@0:     if run_args.user_bin is not None:
kkonganti@0:         run_args.bin = True
kkonganti@0:         arg_bins = run_args.user_bin
kkonganti@0: 
kkonganti@20:     logging.basicConfig(filename="lexmapr_run.log", level=logging.DEBUG)
kkonganti@0: 
kkonganti@0:     if run_args.graph_only:
kkonganti@0:         try:
kkonganti@20:             mapping_results = pandas.read_csv(run_args.input, delimiter="\t")
kkonganti@0:         except:
kkonganti@20:             sys.exit("Input file not readable or not in expected format")
kkonganti@20:         needed_columns = ["Matched_Components", "Match_Status (Macro Level)"] + list(
kkonganti@20:             arg_bins.keys()
kkonganti@20:         )
kkonganti@0:         missing_columns = set(needed_columns).difference(set(mapping_results.columns))
kkonganti@0:         if missing_columns:
kkonganti@20:             sys.exit(f"Missing column(s) {missing_columns} from input file")
kkonganti@0:         t0 = datetime.datetime.now()
kkonganti@20:         logging.info(f"Run start: {t0}")
kkonganti@20:         logging.info("Graphing only")
kkonganti@20:         print("\nGraphing only...")
kkonganti@0:         lexmapr.run_summary.figure_folder()
kkonganti@0:         lexmapr.run_summary.report_results(run_args.input, list(arg_bins.keys()))
kkonganti@0:         lexmapr.run_summary.visualize_results(run_args.input, list(arg_bins.keys()))
kkonganti@20:         print("\t" + f"Done! {datetime.datetime.now()-t0} passed".ljust(60) + "\n")
kkonganti@0:     else:
kkonganti@20:         logging.info(f"Run start: {datetime.datetime.now()}")
kkonganti@0:         lexmapr.pipeline.run(run_args)
kkonganti@0: 
kkonganti@20:     logging.info(f"Run end: {datetime.datetime.now()}\n")