Mercurial > repos > bimib > cobraxy
comparison COBRAxy/custom_data_generator.py @ 353:d13b39f183a5 draft
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| author | francesco_lapi |
|---|---|
| date | Thu, 04 Sep 2025 23:03:26 +0000 |
| parents | 14be2a1071c7 |
| children | 62de44378930 |
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| 352:14be2a1071c7 | 353:d13b39f183a5 |
|---|---|
| 41 help="Output format: CSV (tabular) or Excel (xlsx)") | 41 help="Output format: CSV (tabular) or Excel (xlsx)") |
| 42 | 42 |
| 43 parser.add_argument('-idop', '--output_path', type = str, default='result', | 43 parser.add_argument('-idop', '--output_path', type = str, default='result', |
| 44 help = 'output path for the result files (default: result)') | 44 help = 'output path for the result files (default: result)') |
| 45 | 45 |
| 46 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__), | |
| 47 help="Tool directory (passed from Galaxy as $__tool_directory__)") | |
| 48 | |
| 49 | |
| 46 | 50 |
| 47 return parser.parse_args(args) | 51 return parser.parse_args(args) |
| 48 | 52 |
| 49 ################################- INPUT DATA LOADING -################################ | 53 ################################- INPUT DATA LOADING -################################ |
| 50 def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model: | 54 def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model: |
| 215 except KeyError: | 219 except KeyError: |
| 216 raise utils.ArgsErr("model", "one of Recon/ENGRO2/HMRcore/Custom_model", ARGS.model) | 220 raise utils.ArgsErr("model", "one of Recon/ENGRO2/HMRcore/Custom_model", ARGS.model) |
| 217 | 221 |
| 218 # Load built-in model (Model.getCOBRAmodel uses tool_dir to locate local models) | 222 # Load built-in model (Model.getCOBRAmodel uses tool_dir to locate local models) |
| 219 try: | 223 try: |
| 220 model = model_enum.getCOBRAmodel() | 224 model = model_enum.getCOBRAmodel(toolDir=ARGS.tool_dir) |
| 221 except Exception as e: | 225 except Exception as e: |
| 222 # Wrap/normalize load errors as DataErr for consistency | 226 # Wrap/normalize load errors as DataErr for consistency |
| 223 raise utils.DataErr(ARGS.model, f"failed loading built-in model: {e}") | 227 raise utils.DataErr(ARGS.model, f"failed loading built-in model: {e}") |
| 224 | 228 |
| 225 # Determine final model name: explicit --name overrides, otherwise use the model id | 229 # Determine final model name: explicit --name overrides, otherwise use the model id |