Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_to_bounds.py @ 508:ca98c149ec61 draft

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Uploaded
author francesco_lapi
date Wed, 01 Oct 2025 14:21:26 +0000
parents 20e135a73cad
children
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507:20e135a73cad 508:ca98c149ec61
171 try: 171 try:
172 if file_format == 'tabular' or file_format == 'csv': 172 if file_format == 'tabular' or file_format == 'csv':
173 # Special handling for tabular format using utils functions 173 # Special handling for tabular format using utils functions
174 filepath = os.path.join(output_folder, f"{filename}.csv") 174 filepath = os.path.join(output_folder, f"{filename}.csv")
175 175
176 rules = modelUtils.generate_rules(model, asParsed = False) 176 # Use unified function for tabular export
177 reactions = modelUtils.generate_reactions(model, asParsed = False) 177 merged = modelUtils.export_model_to_tabular(
178 bounds = modelUtils.generate_bounds(model) 178 model=model,
179 medium = modelUtils.get_medium(model) 179 output_path=filepath,
180 180 include_objective=True
181 compartments = modelUtils.generate_compartments(model) 181 )
182
183 df_rules = pd.DataFrame(list(rules.items()), columns = ["ReactionID", "GPR"])
184 df_reactions = pd.DataFrame(list(reactions.items()), columns = ["ReactionID", "Formula"])
185 df_bounds = bounds.reset_index().rename(columns = {"index": "ReactionID"})
186 df_medium = medium.rename(columns = {"reaction": "ReactionID"})
187 df_medium["InMedium"] = True
188
189 merged = df_reactions.merge(df_rules, on = "ReactionID", how = "outer")
190 merged = merged.merge(df_bounds, on = "ReactionID", how = "outer")
191 # Add compartments only if they exist
192 if compartments is not None:
193 merged = merged.merge(compartments, on = "ReactionID", how = "outer")
194
195 merged = merged.merge(df_medium, on = "ReactionID", how = "left")
196 merged["InMedium"] = merged["InMedium"].fillna(False)
197 merged = merged.sort_values(by = "InMedium", ascending = False)
198
199 merged.to_csv(filepath, sep="\t", index=False)
200 182
201 else: 183 else:
202 # Standard COBRA formats 184 # Standard COBRA formats
203 filepath = os.path.join(output_folder, f"{filename}.{file_format}") 185 filepath = os.path.join(output_folder, f"{filename}.{file_format}")
204 186