Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_to_bounds.py @ 218:8d1988935e1f draft

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Uploaded
author luca_milaz
date Sat, 14 Dec 2024 18:50:08 +0000
parents b162b98f9de5
children 264a10b57481
comparison
equal deleted inserted replaced
217:f9deb464e6a6 218:8d1988935e1f
156 Returns: 156 Returns:
157 None 157 None
158 """ 158 """
159 bounds = pd.DataFrame([(rxn.lower_bound, rxn.upper_bound) for rxn in model.reactions], index=rxns_ids, columns=["lower_bound", "upper_bound"]) 159 bounds = pd.DataFrame([(rxn.lower_bound, rxn.upper_bound) for rxn in model.reactions], index=rxns_ids, columns=["lower_bound", "upper_bound"])
160 new_bounds = apply_ras_bounds(bounds, ras_row) 160 new_bounds = apply_ras_bounds(bounds, ras_row)
161 if new_bounds.isnull().values.any():
162 warning(f"RAS values for {cellName} contain NaN values. Skipping this cell.")
161 new_bounds.to_csv(output_folder + cellName + ".csv", sep='\t', index=True) 163 new_bounds.to_csv(output_folder + cellName + ".csv", sep='\t', index=True)
162 pass 164 pass
163 165
164 def generate_bounds(model: cobra.Model, medium: dict, ras=None, output_folder='output/') -> pd.DataFrame: 166 def generate_bounds(model: cobra.Model, medium: dict, ras=None, output_folder='output/') -> pd.DataFrame:
165 """ 167 """