Mercurial > repos > bimib > cobraxy

comparison COBRAxy/fromCSVtoCOBRA_beta.py @ 455:4e2bc80764b6 draft

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Uploaded
author francesco_lapi
date Fri, 12 Sep 2025 15:05:54 +0000
parents 3654c08668f1
children a6e45049c1b9
comparison
equal deleted inserted replaced
454:3654c08668f1 455:4e2bc80764b6
61 # Basic sanity checks 61 # Basic sanity checks
62 if not os.path.exists(ARGS.input): 62 if not os.path.exists(ARGS.input):
63 logging.error('Input file not found: %s', ARGS.input) 63 logging.error('Input file not found: %s', ARGS.input)
64 64
65 out_dir = os.path.dirname(os.path.abspath(ARGS.output)) 65 out_dir = os.path.dirname(os.path.abspath(ARGS.output))
66
66 if out_dir and not os.path.isdir(out_dir): 67 if out_dir and not os.path.isdir(out_dir):
67 try: 68 try:
68 os.makedirs(out_dir, exist_ok=True) 69 os.makedirs(out_dir, exist_ok=True)
69 logging.info('Created missing output directory: %s', out_dir) 70 logging.info('Created missing output directory: %s', out_dir)
70 except Exception as e: 71 except Exception as e:
71 logging.exception('Cannot create output directory: %s', out_dir) 72 logging.exception('Cannot create output directory: %s', out_dir)
72 73
73 # Build the model from the CSV (NOTE: use ARGS.input here)
74 model = modelUtils.build_cobra_model_from_csv(ARGS.input) 74 model = modelUtils.build_cobra_model_from_csv(ARGS.input)
75 75
76 # Save model in requested format 76 # Save model in requested format
77 if ARGS.format == "sbml": 77 if ARGS.format == "sbml":
78 cobra.io.write_sbml_model(model, ARGS.output) 78 cobra.io.write_sbml_model(model, ARGS.output)