Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_simulation_beta.py @ 473:05a80f8e0574 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author luca_milaz
date Mon, 22 Sep 2025 15:32:47 +0000
parents 46901af8df7c
children 6a88ae3f936f
comparison
equal deleted inserted replaced
472:00f2f3437ea3 473:05a80f8e0574
76 help='choose sampling algorithm') 76 help='choose sampling algorithm')
77 77
78 parser.add_argument('-th', '--thinning', 78 parser.add_argument('-th', '--thinning',
79 type=int, 79 type=int,
80 default=100, 80 default=100,
81 required=False, 81 required=True,
82 help='choose thinning') 82 help='choose thinning')
83 83
84 parser.add_argument('-ns', '--n_samples', 84 parser.add_argument('-ns', '--n_samples',
85 type=int, 85 type=int,
86 required=True, 86 required=True,
97 help='choose how many batches') 97 help='choose how many batches')
98 98
99 parser.add_argument('-opt', '--perc_opt', 99 parser.add_argument('-opt', '--perc_opt',
100 type=float, 100 type=float,
101 default=0.9, 101 default=0.9,
102 required=False, 102 required=True,
103 help='choose the fraction of optimality for FVA (0-1)') 103 help='choose the fraction of optimality for FVA (0-1)')
104 104
105 parser.add_argument('-ot', '--output_type', 105 parser.add_argument('-ot', '--output_type',
106 type=str, 106 type=str,
107 required=True, 107 required=True,
346 346
347 Returns: 347 Returns:
348 List[pd.DataFrame]: A list of DataFrames containing statistics and analysis results. 348 List[pd.DataFrame]: A list of DataFrames containing statistics and analysis results.
349 """ 349 """
350 350
351 if ARGS.sampling_enabled == "true" and ARGS.n_samples > 0: 351 if ARGS.sampling_enabled == "true":
352 352
353 if ARGS.algorithm == 'OPTGP': 353 if ARGS.algorithm == 'OPTGP':
354 OPTGP_sampler(model_input, cell_name, ARGS.n_samples, ARGS.thinning, ARGS.n_batches, ARGS.seed) 354 OPTGP_sampler(model_input, cell_name, ARGS.n_samples, ARGS.thinning, ARGS.n_batches, ARGS.seed)
355 elif ARGS.algorithm == 'CBS': 355 elif ARGS.algorithm == 'CBS':
356 CBS_sampler(model_input, cell_name, ARGS.n_samples, ARGS.n_batches, ARGS.seed) 356 CBS_sampler(model_input, cell_name, ARGS.n_samples, ARGS.n_batches, ARGS.seed)
497 ARGS.output_types = ARGS.output_type.split(",") if ARGS.output_type else [] 497 ARGS.output_types = ARGS.output_type.split(",") if ARGS.output_type else []
498 # optional analysis output types -> list or empty 498 # optional analysis output types -> list or empty
499 ARGS.output_type_analysis = ARGS.output_type_analysis.split(",") if ARGS.output_type_analysis else [] 499 ARGS.output_type_analysis = ARGS.output_type_analysis.split(",") if ARGS.output_type_analysis else []
500 500
501 # Determine if sampling should be performed 501 # Determine if sampling should be performed
502 if ARGS.sampling_enabled == "true" and ARGS.n_samples > 0: 502 if ARGS.sampling_enabled == "true":
503 perform_sampling = True 503 perform_sampling = True
504 504
505 print("=== INPUT FILES ===") 505 print("=== INPUT FILES ===")
506 print(f"{ARGS.input_files}") 506 print(f"{ARGS.input_files}")
507 print(f"{ARGS.file_names}") 507 print(f"{ARGS.file_names}")