Mercurial > repos > bimib > cobraxy
comparison COBRAxy/ras_generator.py @ 513:b02cfa3b36dd draft
Uploaded
| author | francesco_lapi |
|---|---|
| date | Wed, 08 Oct 2025 13:01:47 +0000 |
| parents | f32d3c9089fc |
| children | 6acd64232dad |
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| 512:f32d3c9089fc | 513:b02cfa3b36dd |
|---|---|
| 307 rules_total_string=list(set(rules_total_string.split(" "))) | 307 rules_total_string=list(set(rules_total_string.split(" "))) |
| 308 | 308 |
| 309 if any(dataset.index.duplicated(keep=False)): | 309 if any(dataset.index.duplicated(keep=False)): |
| 310 genes_duplicates=orig_gene_list[dataset.index.duplicated(keep=False)] | 310 genes_duplicates=orig_gene_list[dataset.index.duplicated(keep=False)] |
| 311 genes_duplicates_in_model=[elem for elem in genes_duplicates if elem in rules_total_string] | 311 genes_duplicates_in_model=[elem for elem in genes_duplicates if elem in rules_total_string] |
| 312 | |
| 312 if len(genes_duplicates_in_model)>0:#metabolic genes have duplicated entries in the dataset | 313 if len(genes_duplicates_in_model)>0:#metabolic genes have duplicated entries in the dataset |
| 313 list_str=", ".join(genes_duplicates_in_model) | 314 list_str=", ".join(genes_duplicates_in_model) |
| 314 raise ValueError(f"ERROR: Duplicate entries in the gene dataset present in one or more GPR. The following metabolic genes are duplicated: "+list_str) | 315 list_genes=f"ERROR: Duplicate entries in the gene dataset present in one or more GPR. The following metabolic genes are duplicated: "+list_str |
| 316 raise ValueError(list_genes) | |
| 317 else: | |
| 318 list_str=", ".join(genes_duplicates) | |
| 319 list_genes=f"INFO: Duplicate entries in the gene dataset. The following genes are duplicated in the dataset but not mentioned in the GPRs: "+list_str | |
| 320 utils.logWarning(list_genes,ARGS.out_log) | |
| 315 | 321 |
| 316 #check if nan value must be ignored in the GPR | 322 #check if nan value must be ignored in the GPR |
| 317 if ARGS.none: | 323 if ARGS.none: |
| 318 # #e.g. (A or nan --> A) | 324 # #e.g. (A or nan --> A) |
| 319 ignore_nan = True | 325 ignore_nan = True |
| 333 | 339 |
| 334 #report genes not present in the data | 340 #report genes not present in the data |
| 335 if len(genes_not_mapped)>0: | 341 if len(genes_not_mapped)>0: |
| 336 genes_not_mapped_str=", ".join(genes_not_mapped) | 342 genes_not_mapped_str=", ".join(genes_not_mapped) |
| 337 utils.logWarning( | 343 utils.logWarning( |
| 338 f"The following genes are mentioned in the GPR rules but don't appear in the dataset: "+genes_not_mapped_str, | 344 f"INFO: The following genes are mentioned in the GPR rules but don't appear in the dataset: "+genes_not_mapped_str, |
| 339 ARGS.out_log) | 345 ARGS.out_log) |
| 340 | 346 |
| 341 print("Execution succeeded") | 347 print("Execution succeeded") |
| 342 | 348 |
| 343 ############################################################################### | 349 ############################################################################### |