Mercurial > repos > bimib > marea_2_0

comparison marea_2_0/model_generator.py @ 260:29bda13a88a9 draft

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author luca_milaz
date Mon, 08 Jul 2024 15:59:28 +0000
parents 9d85c019db24
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259:58a61b3ebda7 260:29bda13a88a9
81 81
82 def write_to_file(dataset: pd.DataFrame, name: str, keep_index:bool=False)->None: 82 def write_to_file(dataset: pd.DataFrame, name: str, keep_index:bool=False)->None:
83 dataset.to_csv(ARGS.output_folder + name + ".csv", sep = '\t', index = keep_index) 83 dataset.to_csv(ARGS.output_folder + name + ".csv", sep = '\t', index = keep_index)
84 84
85 85
86 def generate_model(model, cell_name, ras, medium, output_model_format)->cobra.: 86 def generate_model(model, cell_name, ras, medium, output_model_format):
87 model_new = model.copy() 87 model_new = model.copy()
88 rxns_ids = [] 88 rxns_ids = []
89 for rxn in model.reactions: 89 for rxn in model.reactions:
90 rxns_ids.append(rxn.id) 90 rxns_ids.append(rxn.id)
91 for reaction in medium.keys(): 91 for reaction in medium.keys():