Mercurial > repos > bimib > cobraxy

comparison COBRAxy/src/exportMetabolicModel.py @ 540:7d5b35c715e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author francesco_lapi
date Sat, 25 Oct 2025 15:08:19 +0000
parents
children fcdbc81feb45
comparison
equal deleted inserted replaced
539:2fb97466e404 540:7d5b35c715e8
1 """
2 Convert a tabular (CSV/TSV/Tabular) description of a COBRA model into a COBRA file.
3
4 Supported output formats: SBML, JSON, MATLAB (.mat), YAML.
5 The script logs to a user-provided file for easier debugging in Galaxy.
6 """
7
8 import os
9 import cobra
10 import argparse
11 from typing import List
12 import logging
13 import utils.model_utils as modelUtils
14
15 ARGS : argparse.Namespace
16 def process_args(args: List[str] = None) -> argparse.Namespace:
17 """
18 Parse command-line arguments for the CSV-to-COBRA conversion tool.
19
20 Returns:
21 argparse.Namespace: Parsed arguments.
22 """
23 parser = argparse.ArgumentParser(
24 usage="%(prog)s [options]",
25 description="Convert a tabular/CSV file to a COBRA model"
26 )
27
28
29 parser.add_argument("--out_log", type=str, required=True,
30 help="Output log file")
31
32
33 parser.add_argument("--input", type=str, required=True,
34 help="Input tabular file (CSV/TSV)")
35
36
37 parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
38 help="Model format (SBML, JSON, MATLAB, YAML)")
39
40
41 parser.add_argument("--output", type=str, required=True,
42 help="Output model file path")
43
44 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
45 help="Tool directory (passed from Galaxy as $__tool_directory__)")
46
47
48 return parser.parse_args(args)
49
50
51 ###############################- ENTRY POINT -################################
52
53 def main(args: List[str] = None) -> None:
54 """
55 Entry point: parse arguments, build the COBRA model from a CSV/TSV file,
56 and save it in the requested format.
57
58 Returns:
59 None
60 """
61 global ARGS
62 ARGS = process_args(args)
63
64 # configure logging to the requested log file (overwrite each run)
65 logging.basicConfig(filename=ARGS.out_log,
66 level=logging.DEBUG,
67 format='%(asctime)s %(levelname)s: %(message)s',
68 filemode='w')
69
70 logging.info('Starting fromCSVtoCOBRA tool')
71 logging.debug('Args: input=%s format=%s output=%s tool_dir=%s', ARGS.input, ARGS.format, ARGS.output, ARGS.tool_dir)
72
73 try:
74 # Basic sanity checks
75 if not os.path.exists(ARGS.input):
76 logging.error('Input file not found: %s', ARGS.input)
77
78 out_dir = os.path.dirname(os.path.abspath(ARGS.output))
79
80 if out_dir and not os.path.isdir(out_dir):
81 try:
82 os.makedirs(out_dir, exist_ok=True)
83 logging.info('Created missing output directory: %s', out_dir)
84 except Exception as e:
85 logging.exception('Cannot create output directory: %s', out_dir)
86
87 model = modelUtils.build_cobra_model_from_csv(ARGS.input)
88
89
90 logging.info('Created model with name: %s (ID: %s)', model.name, model.id)
91
92 # Save model in requested format - Galaxy handles the filename
93 if ARGS.format == "sbml":
94 cobra.io.write_sbml_model(model, ARGS.output)
95 elif ARGS.format == "json":
96 cobra.io.save_json_model(model, ARGS.output)
97 elif ARGS.format == "mat":
98 cobra.io.save_matlab_model(model, ARGS.output)
99 elif ARGS.format == "yaml":
100 cobra.io.save_yaml_model(model, ARGS.output)
101 else:
102 logging.error('Unknown format requested: %s', ARGS.format)
103 raise ValueError(f"Unknown format: {ARGS.format}")
104
105
106 logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)
107 print(f"Model created successfully in {ARGS.format.upper()} format")
108
109 except Exception as e:
110 # Log full traceback to the out_log so Galaxy users/admins can see what happened
111 logging.exception('Unhandled exception in fromCSVtoCOBRA')
112 print(f"ERROR: {str(e)}")
113 raise
114
115
116 if __name__ == '__main__':
117 main()