Mercurial > repos > bimib > cobraxy

comparison COBRAxy/custom_data_generator.py @ 359:820befcfb42f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author francesco_lapi
date Thu, 04 Sep 2025 23:27:52 +0000
parents be93df100d60
children ca5d82f9075f
comparison
equal deleted inserted replaced
358:3fc99f6b7668 359:820befcfb42f
20 description="Generate custom data from a given model" 20 description="Generate custom data from a given model"
21 ) 21 )
22 22
23 parser.add_argument("--out_log", type=str, required=True, 23 parser.add_argument("--out_log", type=str, required=True,
24 help="Output log file") 24 help="Output log file")
25 parser.add_argument("--out_data", type=str, required=True,
26 help="Single output dataset (CSV or Excel)")
27 25
28 parser.add_argument("--model", type=str, 26 parser.add_argument("--model", type=str,
29 help="Built-in model identifier (e.g., ENGRO2, Recon, HMRcore)") 27 help="Built-in model identifier (e.g., ENGRO2, Recon, HMRcore)")
30 parser.add_argument("--input", type=str, 28 parser.add_argument("--input", type=str,
31 help="Custom model file (JSON or XML)") 29 help="Custom model file (JSON or XML)")
249 247
250 merged["InMedium"] = merged["InMedium"].fillna(False) 248 merged["InMedium"] = merged["InMedium"].fillna(False)
251 249
252 merged = merged.sort_values(by = "InMedium", ascending = False) 250 merged = merged.sort_values(by = "InMedium", ascending = False)
253 251
254 out_file = os.path.join(ARGS.output_path, f"{os.path.basename(ARGS.name).split('.')[0]}_custom_data") 252 #out_file = os.path.join(ARGS.output_path, f"{os.path.basename(ARGS.name).split('.')[0]}_custom_data")
255 253
256 #merged.to_csv(out_file, sep = '\t', index = False) 254 #merged.to_csv(out_file, sep = '\t', index = False)
257 255
258 256
259 #### 257 ####
260 out_data_path = ARGS.out_data 258 out_data_path = ARGS.output_path
261 259
262 if ARGS.output_format == "xlsx": 260 if ARGS.output_format == "xlsx":
263 merged.to_excel(out_data_path, index=False) 261 merged.to_excel(out_data_path, index=False)
264 else: 262 else:
265 merged.to_csv(out_data_path, sep="\t", index=False) 263 merged.to_csv(out_data_path, sep="\t", index=False)