Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_simulation_beta.py @ 430:f49c951c9fe6 draft

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Uploaded
author francesco_lapi
date Wed, 10 Sep 2025 14:53:36 +0000
parents 27c5a67f1ee6
children a6e45049c1b9
comparison
equal deleted inserted replaced
429:0485c4b1943d 430:f49c951c9fe6
77 77
78 parser.add_argument('-nb', '--n_batches', 78 parser.add_argument('-nb', '--n_batches',
79 type = int, 79 type = int,
80 required = True, 80 required = True,
81 help = 'choose how many batches') 81 help = 'choose how many batches')
82
83 parser.add_argument('-opt', '--perc_opt',
84 type = float,
85 default=0.9,
86 required = False,
87 help = 'choose the fraction of optimality for FVA (0-1)')
82 88
83 parser.add_argument('-ot', '--output_type', 89 parser.add_argument('-ot', '--output_type',
84 type = str, 90 type = str,
85 required = True, 91 required = True,
86 help = 'output type') 92 help = 'output type')
357 df_pFBA.loc[0,[rxn.id for rxn in model.reactions]] = fluxes.tolist() 363 df_pFBA.loc[0,[rxn.id for rxn in model.reactions]] = fluxes.tolist()
358 df_pFBA = df_pFBA.reset_index(drop=True) 364 df_pFBA = df_pFBA.reset_index(drop=True)
359 df_pFBA.index = [model_name] 365 df_pFBA.index = [model_name]
360 df_pFBA = df_pFBA.astype(float).round(6) 366 df_pFBA = df_pFBA.astype(float).round(6)
361 elif(output_type == "FVA"): 367 elif(output_type == "FVA"):
362 fva = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8) 368 fva = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=ARGS.perc_opt, processes=1).round(8)
363 columns = [] 369 columns = []
364 for rxn in fva.index.to_list(): 370 for rxn in fva.index.to_list():
365 columns.append(rxn + "_min") 371 columns.append(rxn + "_min")
366 columns.append(rxn + "_max") 372 columns.append(rxn + "_max")
367 df_FVA= pd.DataFrame(columns = columns) 373 df_FVA= pd.DataFrame(columns = columns)