Mercurial > repos > bimib > cobraxy

comparison COBRAxy/tabular2MetabolicModel.py @ 491:7a413a5ec566 draft

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author francesco_lapi
date Mon, 29 Sep 2025 15:34:59 +0000
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children df90f40a156c
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490:c6ea189ea7e9 491:7a413a5ec566
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
45 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
46 help="Tool directory (passed from Galaxy as $__tool_directory__)")
47
48
49 return parser.parse_args(args)
50
51
52 ###############################- ENTRY POINT -################################
53
54 def main(args: List[str] = None) -> None:
55 """
56 Entry point: parse arguments, build the COBRA model from a CSV/TSV file,
57 and save it in the requested format.
58
59 Returns:
60 None
61 """
62 global ARGS
63 ARGS = process_args(args)
64
65 # configure logging to the requested log file (overwrite each run)
66 logging.basicConfig(filename=ARGS.out_log,
67 level=logging.DEBUG,
68 format='%(asctime)s %(levelname)s: %(message)s',
69 filemode='w')
70
71 logging.info('Starting fromCSVtoCOBRA tool')
72 logging.debug('Args: input=%s format=%s output=%s tool_dir=%s', ARGS.input, ARGS.format, ARGS.output, ARGS.tool_dir)
73
74 try:
75 # Basic sanity checks
76 if not os.path.exists(ARGS.input):
77 logging.error('Input file not found: %s', ARGS.input)
78
79 out_dir = os.path.dirname(os.path.abspath(ARGS.output))
80
81 if out_dir and not os.path.isdir(out_dir):
82 try:
83 os.makedirs(out_dir, exist_ok=True)
84 logging.info('Created missing output directory: %s', out_dir)
85 except Exception as e:
86 logging.exception('Cannot create output directory: %s', out_dir)
87
88 model = modelUtils.build_cobra_model_from_csv(ARGS.input)
89
90 # Save model in requested format
91 if ARGS.format == "sbml":
92 cobra.io.write_sbml_model(model, ARGS.output)
93 elif ARGS.format == "json":
94 cobra.io.save_json_model(model, ARGS.output)
95 elif ARGS.format == "mat":
96 cobra.io.save_matlab_model(model, ARGS.output)
97 elif ARGS.format == "yaml":
98 cobra.io.save_yaml_model(model, ARGS.output)
99 else:
100 logging.error('Unknown format requested: %s', ARGS.format)
101 print(f"ERROR: Unknown format: {ARGS.format}")
102
103
104 logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)
105
106 except Exception:
107 # Log full traceback to the out_log so Galaxy users/admins can see what happened
108 logging.exception('Unhandled exception in fromCSVtoCOBRA')
109
110
111 if __name__ == '__main__':
112 main()