Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_simulation.py @ 159:898f2641d3f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author francesco_lapi
date Tue, 12 Nov 2024 16:58:48 +0000
parents 30acaa01df61
children e1b0ddc770a9
comparison
equal deleted inserted replaced
158:30acaa01df61 159:898f2641d3f7
86 parser.add_argument('-ota', '--output_type_analysis', 86 parser.add_argument('-ota', '--output_type_analysis',
87 type = str, 87 type = str,
88 required = False, 88 required = False,
89 help = 'output type analysis') 89 help = 'output type analysis')
90 90
91 parser.add_argument( 91 parser.add_argument('-idop', '--output_path',
92 '-idop', '--output_path', 92 type = str,
93 type = str, 93 default='flux_simulation',
94 default='flux_simulation', 94 help = 'output path for maps')
95 help = 'output path for maps')
96 95
97 ARGS = parser.parse_args(args) 96 ARGS = parser.parse_args(args)
98 return ARGS 97 return ARGS
99 98
100 ########################### warning ########################################### 99 ########################### warning ###########################################
237 bounds_df = read_dataset(bounds_path, "bounds dataset") 236 bounds_df = read_dataset(bounds_path, "bounds dataset")
238 for rxn_index, row in bounds_df.iterrows(): 237 for rxn_index, row in bounds_df.iterrows():
239 model_input.reactions.get_by_id(rxn_index).lower_bound = row.lower_bound 238 model_input.reactions.get_by_id(rxn_index).lower_bound = row.lower_bound
240 model_input.reactions.get_by_id(rxn_index).upper_bound = row.upper_bound 239 model_input.reactions.get_by_id(rxn_index).upper_bound = row.upper_bound
241 240
242 name = cell_name 241 name = cell_name.split('.')[0]
243 242
244 if ARGS.algorithm == 'OPTGP': 243 if ARGS.algorithm == 'OPTGP':
245 OPTGP_sampler(model_input, name, ARGS.n_samples, ARGS.thinning, ARGS.n_batches, ARGS.seed) 244 OPTGP_sampler(model_input, name, ARGS.n_samples, ARGS.thinning, ARGS.n_batches, ARGS.seed)
246 245
247 elif ARGS.algorithm == 'CBS': 246 elif ARGS.algorithm == 'CBS':
380 num_processors = cpu_count() 379 num_processors = cpu_count()
381 380
382 global ARGS 381 global ARGS
383 ARGS = process_args(args) 382 ARGS = process_args(args)
384 383
385 if not os.path.exists('flux_simulation/'): 384 if not os.path.exists(ARGS.output_path):
386 os.makedirs('flux_simulation/') 385 os.makedirs(ARGS.output_path)
387
388 386
389 model_type :utils.Model = ARGS.model_selector 387 model_type :utils.Model = ARGS.model_selector
390 if model_type is utils.Model.Custom: 388 if model_type is utils.Model.Custom:
391 model = model_type.getCOBRAmodel(customPath = utils.FilePath.fromStrPath(ARGS.model), customExtension = utils.FilePath.fromStrPath(ARGS.model_name).ext) 389 model = model_type.getCOBRAmodel(customPath = utils.FilePath.fromStrPath(ARGS.model), customExtension = utils.FilePath.fromStrPath(ARGS.model_name).ext)
392 else: 390 else: