Mercurial > repos > bimib > cobraxy

comparison COBRAxy/metabolicModel2Tabular.py @ 498:df90f40a156c draft

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Uploaded
author francesco_lapi
date Tue, 30 Sep 2025 16:13:08 +0000
parents 36838126cc07
children 054c872e3880
comparison
equal deleted inserted replaced
497:36838126cc07 498:df90f40a156c
34 help="Output log file") 34 help="Output log file")
35 35
36 parser.add_argument("--model", type=str, 36 parser.add_argument("--model", type=str,
37 help="Built-in model identifier (e.g., ENGRO2, Recon, HMRcore)") 37 help="Built-in model identifier (e.g., ENGRO2, Recon, HMRcore)")
38 parser.add_argument("--input", type=str, 38 parser.add_argument("--input", type=str,
39 help="Custom model file (JSON or XML)") 39 help="Custom model file (JSON, XML, MAT, YAML)")
40 parser.add_argument("--name", nargs='*', required=True, 40 parser.add_argument("--name", nargs='*', required=True,
41 help="Model name (default or custom)") 41 help="Model name (default or custom)")
42 42
43 parser.add_argument("--medium_selector", type=str, required=True, 43 parser.add_argument("--medium_selector", type=str, required=True,
44 help="Medium selection option") 44 help="Medium selection option")
54 54
55 55
56 return parser.parse_args(args) 56 return parser.parse_args(args)
57 57
58 ################################- INPUT DATA LOADING -################################ 58 ################################- INPUT DATA LOADING -################################
59 def detect_file_format(file_path: str) -> utils.FileFormat:
60 """
61 Detect file format by examining file content and extension.
62 Handles Galaxy .dat files by looking at content.
63 """
64 try:
65 with open(file_path, 'r') as f:
66 first_lines = ''.join([f.readline() for _ in range(5)])
67
68 # Check for XML (SBML)
69 if '<?xml' in first_lines or '<sbml' in first_lines:
70 return utils.FileFormat.XML
71
72 # Check for JSON
73 if first_lines.strip().startswith('{'):
74 return utils.FileFormat.JSON
75
76 # Check for YAML
77 if any(line.strip().endswith(':') for line in first_lines.split('\n')[:3]):
78 return utils.FileFormat.YML
79
80 except:
81 pass
82
83 # Fall back to extension-based detection
84 if file_path.endswith('.xml') or file_path.endswith('.sbml'):
85 return utils.FileFormat.XML
86 elif file_path.endswith('.json'):
87 return utils.FileFormat.JSON
88 elif file_path.endswith('.mat'):
89 return utils.FileFormat.MAT
90 elif file_path.endswith('.yml') or file_path.endswith('.yaml'):
91 return utils.FileFormat.YML
92
93 # Default to XML for unknown extensions
94 return utils.FileFormat.XML
95
59 def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model: 96 def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model:
60 """ 97 """
61 Loads a custom model from a file, either in JSON, XML, MAT, or YML format. 98 Loads a custom model from a file, either in JSON, XML, MAT, or YML format.
62 99
63 Args: 100 Args:
184 # Convert name from list to string (handles names with spaces) 221 # Convert name from list to string (handles names with spaces)
185 if isinstance(ARGS.name, list): 222 if isinstance(ARGS.name, list):
186 ARGS.name = ' '.join(ARGS.name) 223 ARGS.name = ' '.join(ARGS.name)
187 224
188 if ARGS.input: 225 if ARGS.input:
189 # Load a custom model from file 226 # Load a custom model from file with auto-detected format
190 model = load_custom_model( 227 detected_format = detect_file_format(ARGS.input)
191 utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.input).ext) 228 model = load_custom_model(utils.FilePath.fromStrPath(ARGS.input), detected_format)
192 else: 229 else:
193 # Load a built-in model 230 # Load a built-in model
194 if not ARGS.model: 231 if not ARGS.model:
195 raise utils.ArgsErr("model", "either --model or --input must be provided", "None") 232 raise utils.ArgsErr("model", "either --model or --input must be provided", "None")
196 233