comparison COBRAxy/ras_to_bounds.py @ 219:264a10b57481 draft

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author luca_milaz
date Sat, 14 Dec 2024 18:56:53 +0000
parents 8d1988935e1f
children fa5483499199
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218:8d1988935e1f 219:264a10b57481
131 scaling_factor = ras_row[reaction] 131 scaling_factor = ras_row[reaction]
132 lower_bound=bounds.loc[reaction, "lower_bound"] 132 lower_bound=bounds.loc[reaction, "lower_bound"]
133 upper_bound=bounds.loc[reaction, "upper_bound"] 133 upper_bound=bounds.loc[reaction, "upper_bound"]
134 valMax=float((upper_bound)*scaling_factor) 134 valMax=float((upper_bound)*scaling_factor)
135 valMin=float((lower_bound)*scaling_factor) 135 valMin=float((lower_bound)*scaling_factor)
136 if(valMax is None or valMin is None):
137 warning(f"RAS values for {reaction}is None")
136 if upper_bound!=0 and lower_bound==0: 138 if upper_bound!=0 and lower_bound==0:
137 new_bounds.loc[reaction, "upper_bound"] = valMax 139 new_bounds.loc[reaction, "upper_bound"] = valMax
138 if upper_bound==0 and lower_bound!=0: 140 if upper_bound==0 and lower_bound!=0:
139 new_bounds.loc[reaction, "lower_bound"] = valMin 141 new_bounds.loc[reaction, "lower_bound"] = valMin
140 if upper_bound!=0 and lower_bound!=0: 142 if upper_bound!=0 and lower_bound!=0:
158 """ 160 """
159 bounds = pd.DataFrame([(rxn.lower_bound, rxn.upper_bound) for rxn in model.reactions], index=rxns_ids, columns=["lower_bound", "upper_bound"]) 161 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) 162 new_bounds = apply_ras_bounds(bounds, ras_row)
161 if new_bounds.isnull().values.any(): 163 if new_bounds.isnull().values.any():
162 warning(f"RAS values for {cellName} contain NaN values. Skipping this cell.") 164 warning(f"RAS values for {cellName} contain NaN values. Skipping this cell.")
165 return
163 new_bounds.to_csv(output_folder + cellName + ".csv", sep='\t', index=True) 166 new_bounds.to_csv(output_folder + cellName + ".csv", sep='\t', index=True)
164 pass 167 pass
165 168
166 def generate_bounds(model: cobra.Model, medium: dict, ras=None, output_folder='output/') -> pd.DataFrame: 169 def generate_bounds(model: cobra.Model, medium: dict, ras=None, output_folder='output/') -> pd.DataFrame:
167 """ 170 """