Mercurial > repos > bimib > cobraxy
comparison COBRAxy/ras_to_bounds.py @ 506:ffc234ec80db draft
Uploaded
| author | francesco_lapi |
|---|---|
| date | Wed, 01 Oct 2025 13:19:03 +0000 |
| parents | 97eea560a10f |
| children | 20e135a73cad |
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| 505:96f512dff490 | 506:ffc234ec80db |
|---|---|
| 176 rules = modelUtils.generate_rules(model, asParsed = False) | 176 rules = modelUtils.generate_rules(model, asParsed = False) |
| 177 reactions = modelUtils.generate_reactions(model, asParsed = False) | 177 reactions = modelUtils.generate_reactions(model, asParsed = False) |
| 178 bounds = modelUtils.generate_bounds(model) | 178 bounds = modelUtils.generate_bounds(model) |
| 179 medium = modelUtils.get_medium(model) | 179 medium = modelUtils.get_medium(model) |
| 180 | 180 |
| 181 try: | 181 compartments = modelUtils.generate_compartments(model) |
| 182 compartments = modelUtils.generate_compartments(model) | |
| 183 except: | |
| 184 compartments = None | |
| 185 | 182 |
| 186 df_rules = pd.DataFrame(list(rules.items()), columns = ["ReactionID", "Rule"]) | 183 df_rules = pd.DataFrame(list(rules.items()), columns = ["ReactionID", "Rule"]) |
| 187 df_reactions = pd.DataFrame(list(reactions.items()), columns = ["ReactionID", "Reaction"]) | 184 df_reactions = pd.DataFrame(list(reactions.items()), columns = ["ReactionID", "Reaction"]) |
| 188 df_bounds = bounds.reset_index().rename(columns = {"index": "ReactionID"}) | 185 df_bounds = bounds.reset_index().rename(columns = {"index": "ReactionID"}) |
| 189 df_medium = medium.rename(columns = {"reaction": "ReactionID"}) | 186 df_medium = medium.rename(columns = {"reaction": "ReactionID"}) |
| 190 df_medium["InMedium"] = True | 187 df_medium["InMedium"] = True |
| 191 | 188 |
| 192 merged = df_reactions.merge(df_rules, on = "ReactionID", how = "outer") | 189 merged = df_reactions.merge(df_rules, on = "ReactionID", how = "outer") |
| 193 merged = merged.merge(df_bounds, on = "ReactionID", how = "outer") | 190 merged = merged.merge(df_bounds, on = "ReactionID", how = "outer") |
| 194 | 191 # Add compartments only if they exist |
| 195 # Add compartments only if they exist and model name is ENGRO2 | 192 if compartments is not None: |
| 196 if compartments is not None and hasattr(ARGS, 'name') and ARGS.name == "ENGRO2": | |
| 197 merged = merged.merge(compartments, on = "ReactionID", how = "outer") | 193 merged = merged.merge(compartments, on = "ReactionID", how = "outer") |
| 198 | 194 |
| 199 merged = merged.merge(df_medium, on = "ReactionID", how = "left") | 195 merged = merged.merge(df_medium, on = "ReactionID", how = "left") |
| 200 merged["InMedium"] = merged["InMedium"].fillna(False) | 196 merged["InMedium"] = merged["InMedium"].fillna(False) |
| 201 merged = merged.sort_values(by = "InMedium", ascending = False) | 197 merged = merged.sort_values(by = "InMedium", ascending = False) |