Mercurial > repos > bimib > cobraxy

comparison COBRAxy/custom_data_generator.py @ 384:8a1213d1393d draft

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Uploaded
author francesco_lapi
date Fri, 05 Sep 2025 09:53:40 +0000
parents 0a3ca20848f3
children cccbf259459e
comparison
equal deleted inserted replaced
383:d2e36a8ab451 384:8a1213d1393d
34 parser.add_argument("--medium_selector", type=str, required=True, 34 parser.add_argument("--medium_selector", type=str, required=True,
35 help="Medium selection option (default/custom)") 35 help="Medium selection option (default/custom)")
36 parser.add_argument("--medium", type=str, 36 parser.add_argument("--medium", type=str,
37 help="Custom medium file if medium_selector=Custom") 37 help="Custom medium file if medium_selector=Custom")
38 38
39 parser.add_argument("--output_format", type=str, choices=["tabular", "xlsx"], required=True,
40 help="Output format: CSV (tabular) or Excel (xlsx)")
41
42 parser.add_argument("--out_tabular", type=str, 39 parser.add_argument("--out_tabular", type=str,
43 help="Output file for the merged dataset (CSV or XLSX)")
44
45 parser.add_argument("--out_xlsx", type=str,
46 help="Output file for the merged dataset (CSV or XLSX)") 40 help="Output file for the merged dataset (CSV or XLSX)")
47 41
48 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__), 42 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
49 help="Tool directory (passed from Galaxy as $__tool_directory__)") 43 help="Tool directory (passed from Galaxy as $__tool_directory__)")
50 44
197 os.makedirs(os.path.dirname(path) or ".", exist_ok=True) 191 os.makedirs(os.path.dirname(path) or ".", exist_ok=True)
198 df.to_csv(path, sep="\t", index=False) 192 df.to_csv(path, sep="\t", index=False)
199 except Exception as e: 193 except Exception as e:
200 raise utils.DataErr(path, f"failed writing tabular output: {e}") 194 raise utils.DataErr(path, f"failed writing tabular output: {e}")
201 195
202 def save_as_xlsx_df(df: pd.DataFrame, path: str) -> None:
203 try:
204 if not path.lower().endswith(".xlsx"):
205 path += ".xlsx"
206 os.makedirs(os.path.dirname(path) or ".", exist_ok=True)
207 df.to_excel(path, index=False)
208 except Exception as e:
209 raise utils.DataErr(path, f"failed writing xlsx output: {e}")
210 196
211 ###############################- ENTRY POINT -################################ 197 ###############################- ENTRY POINT -################################
212 def main(args:List[str] = None) -> None: 198 def main(args:List[str] = None) -> None:
213 """ 199 """
214 Initializes everything and sets the program in motion based on the fronted input arguments. 200 Initializes everything and sets the program in motion based on the fronted input arguments.
270 #merged.to_csv(out_file, sep = '\t', index = False) 256 #merged.to_csv(out_file, sep = '\t', index = False)
271 257
272 258
273 #### 259 ####
274 260
275 # write only the requested output 261
276 if ARGS.output_format == "xlsx": 262 if not ARGS.out_tabular:
277 if not ARGS.out_xlsx: 263 raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
278 raise utils.ArgsErr("out_xlsx", "output path (--out_xlsx) is required when output_format == xlsx", ARGS.out_xlsx) 264 save_as_tabular_df(merged, ARGS.out_tabular)
279 save_as_xlsx_df(merged, ARGS.out_xlsx) 265 expected = ARGS.out_tabular
280 expected = ARGS.out_xlsx
281 else:
282 if not ARGS.out_tabular:
283 raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
284 save_as_tabular_df(merged, ARGS.out_tabular)
285 expected = ARGS.out_tabular
286 266
287 # verify output exists and non-empty 267 # verify output exists and non-empty
288 if not expected or not os.path.exists(expected) or os.path.getsize(expected) == 0: 268 if not expected or not os.path.exists(expected) or os.path.getsize(expected) == 0:
289 raise utils.DataErr(expected, "Output non creato o vuoto") 269 raise utils.DataErr(expected, "Output non creato o vuoto")
290 270