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1 """Entry script"""
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2
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3 __version__ = '1.0.0'
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4 import argparse, datetime, json, logging, os, pandas, sys
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5 import lexmapr.pipeline, lexmapr.run_summary
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6 from lexmapr.definitions import arg_bins
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7
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8
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9 def valid_input(file_path):
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10 '''Exits if input file is invalid'''
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11 _, file_ext = os.path.splitext(file_path)
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12 if file_ext.lower() != '.csv' and file_ext.lower() != '.tsv':
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13 sys.exit('Please supply a CSV or TSV input file with the correct file extension')
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14 if not os.path.exists(file_path):
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15 sys.exit(f'Input file named \"{file_path}\" not found')
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16 return(file_path.strip())
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17
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18 def valid_json(file_path):
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19 '''Outputs read JSON file and exits if file is invalid'''
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20 try:
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21 with open(file_path, 'r') as JSON_file:
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22 try:
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23 return(json.load(JSON_file))
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24 except(json.decoder.JSONDecodeError):
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25 sys.exit(f'User-defined bins not in readable JSON format')
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26 except(FileNotFoundError):
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27 sys.exit(f'File named \"{file_path}\" not found')
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28
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29 def valid_list(list_str):
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30 '''Return list of user-defined ontologies'''
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31 return([x.strip().upper() for x in list_str.split(',')])
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32
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33 if __name__ == "__main__":
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34 # Parse arguments, initiate log file and start run
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35 arg_parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter)
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36 arg_parser.add_argument('input', help='input CSV or TSV file; required', type=valid_input)
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37 arg_parser.add_argument('-o', '--output', metavar='\b',
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38 help=' output TSV file path; default is stdout')
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39 arg_parser.add_argument('-a', '--no_ancestors', action='store_true',
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40 help='remove ancestral terms from output')
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41 arg_parser.add_argument('-b', '--bin', action='store_true',
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42 help='classify samples into default bins')
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43 arg_parser.add_argument('-e', '--embl_ontol', metavar='\b', type=valid_list,
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44 help=' user-defined comma-separated ontology short names')
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45 arg_parser.add_argument('-f', '--full', action='store_true', help='full output format')
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46 arg_parser.add_argument('-g', '--graph', action='store_true',
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47 help='visualize summaries of mapping and binning')
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48 arg_parser.add_argument('-j', '--graph_only', action='store_true',
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49 help='only perform visualization with LexMapr output')
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50 arg_parser.add_argument('-r', '--remake_cache', action='store_true',
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51 help='remake cached resources')
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52 arg_parser.add_argument('-u', '--user_bin', metavar='\b', type=valid_json,
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53 help=' path to JSON file with user-defined bins')
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54 arg_parser.add_argument('-v', '--version', action='version',
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55 version='%(prog)s '+__version__)
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56
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57 # TODO: encoding argument addded to logging.basicConfig in Python 3.9; now defaults to open()
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58 run_args = arg_parser.parse_args()
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59 if run_args.user_bin is not None:
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60 run_args.bin = True
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61 arg_bins = run_args.user_bin
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62
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63 logging.basicConfig(filename='lexmapr_run.log', level=logging.DEBUG)
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64
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65 if run_args.graph_only:
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66 try:
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67 mapping_results = pandas.read_csv(run_args.input, delimiter='\t')
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68 except:
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69 sys.exit('Input file not readable or not in expected format')
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70 needed_columns = ['Matched_Components','Match_Status (Macro Level)']+list(arg_bins.keys())
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71 missing_columns = set(needed_columns).difference(set(mapping_results.columns))
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72 if missing_columns:
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73 sys.exit(f'Missing column(s) {missing_columns} from input file')
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74 t0 = datetime.datetime.now()
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75 logging.info(f'Run start: {t0}')
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76 logging.info('Graphing only')
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77 print('\nGraphing only...')
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78 lexmapr.run_summary.figure_folder()
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79 lexmapr.run_summary.report_results(run_args.input, list(arg_bins.keys()))
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80 lexmapr.run_summary.visualize_results(run_args.input, list(arg_bins.keys()))
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81 print('\t'+f'Done! {datetime.datetime.now()-t0} passed'.ljust(60)+'\n')
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82 else:
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83 logging.info(f'Run start: {datetime.datetime.now()}')
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84 lexmapr.pipeline.run(run_args)
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85
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86 logging.info(f'Run end: {datetime.datetime.now()}\n')
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