Mercurial > repos > bimib > cobraxy

comparison COBRAxy/src/flux_simulation.py @ 546:01147e83f43c draft

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Uploaded
author luca_milaz
date Mon, 27 Oct 2025 12:33:08 +0000
parents fcdbc81feb45
children 73f2f7e2be17
comparison
equal deleted inserted replaced
545:5a73d813b1db 546:01147e83f43c
63 parser.add_argument('-td', '--tool_dir', 63 parser.add_argument('-td', '--tool_dir',
64 type=str, 64 type=str,
65 default=os.path.dirname(os.path.abspath(__file__)), 65 default=os.path.dirname(os.path.abspath(__file__)),
66 help='your tool directory (default: auto-detected package location)') 66 help='your tool directory (default: auto-detected package location)')
67 67
68 parser.add_argument('-in', '--input', 68 parser.add_argument('-inf', '--input_file',
69 required=True, 69 required=True,
70 type=str, 70 type=str,
71 help='input bounds files or complete model files') 71 help='path to file containing list of input bounds files or complete model files (one per line)')
72 72
73 parser.add_argument('-ni', '--name', 73 parser.add_argument('-nif', '--name_file',
74 required=True, 74 required=True,
75 type=str, 75 type=str,
76 help='cell names') 76 help='path to file containing list of cell names (one per line)')
77 77
78 parser.add_argument('-a', '--algorithm', 78 parser.add_argument('-a', '--algorithm',
79 type=str, 79 type=str,
80 choices=['OPTGP', 'CBS'], 80 choices=['OPTGP', 'CBS'],
81 required=True, 81 required=True,
526 ARGS = process_args(args) 526 ARGS = process_args(args)
527 527
528 if not os.path.exists('flux_simulation'): 528 if not os.path.exists('flux_simulation'):
529 os.makedirs('flux_simulation') 529 os.makedirs('flux_simulation')
530 530
531 # --- Normalize inputs (the tool may pass comma-separated --input and either --name or --names) --- 531 # --- Read input files and names from the provided file paths ---
532 ARGS.input_files = ARGS.input.split(",") if ARGS.input else [] 532 with open(ARGS.input_file, 'r') as f:
533 ARGS.file_names = ARGS.name.split(",") 533 ARGS.input_files = [line.strip() for line in f if line.strip()]
534
535 with open(ARGS.name_file, 'r') as f:
536 ARGS.file_names = [line.strip() for line in f if line.strip()]
537
534 # output types (required) -> list 538 # output types (required) -> list
535 ARGS.output_types = ARGS.output_type.split(",") if ARGS.output_type else [] 539 ARGS.output_types = ARGS.output_type.split(",") if ARGS.output_type else []
536 # optional analysis output types -> list or empty 540 # optional analysis output types -> list or empty
537 ARGS.output_type_analysis = ARGS.output_type_analysis.split(",") if ARGS.output_type_analysis else [] 541 ARGS.output_type_analysis = ARGS.output_type_analysis.split(",") if ARGS.output_type_analysis else []
538 542