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491
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1 """
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2 Convert a tabular (CSV/TSV/Tabular) description of a COBRA model into a COBRA file.
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3
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4 Supported output formats: SBML, JSON, MATLAB (.mat), YAML.
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5 The script logs to a user-provided file for easier debugging in Galaxy.
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6 """
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7
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8 import os
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9 import cobra
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10 import argparse
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11 from typing import List
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12 import logging
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13 import utils.model_utils as modelUtils
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14
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15 ARGS : argparse.Namespace
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16 def process_args(args: List[str] = None) -> argparse.Namespace:
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17 """
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18 Parse command-line arguments for the CSV-to-COBRA conversion tool.
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19
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20 Returns:
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21 argparse.Namespace: Parsed arguments.
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22 """
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23 parser = argparse.ArgumentParser(
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24 usage="%(prog)s [options]",
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25 description="Convert a tabular/CSV file to a COBRA model"
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26 )
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27
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28
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29 parser.add_argument("--out_log", type=str, required=True,
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30 help="Output log file")
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31
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32
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33 parser.add_argument("--input", type=str, required=True,
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34 help="Input tabular file (CSV/TSV)")
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35
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36
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37 parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
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38 help="Model format (SBML, JSON, MATLAB, YAML)")
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39
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40
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41 parser.add_argument("--output", type=str, required=True,
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42 help="Output model file path")
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43
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44
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45 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
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46 help="Tool directory (passed from Galaxy as $__tool_directory__)")
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47
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48
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49 return parser.parse_args(args)
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50
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51
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52 ###############################- ENTRY POINT -################################
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53
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54 def main(args: List[str] = None) -> None:
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55 """
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56 Entry point: parse arguments, build the COBRA model from a CSV/TSV file,
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57 and save it in the requested format.
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58
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59 Returns:
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60 None
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61 """
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62 global ARGS
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63 ARGS = process_args(args)
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64
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65 # configure logging to the requested log file (overwrite each run)
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66 logging.basicConfig(filename=ARGS.out_log,
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67 level=logging.DEBUG,
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68 format='%(asctime)s %(levelname)s: %(message)s',
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69 filemode='w')
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70
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71 logging.info('Starting fromCSVtoCOBRA tool')
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72 logging.debug('Args: input=%s format=%s output=%s tool_dir=%s', ARGS.input, ARGS.format, ARGS.output, ARGS.tool_dir)
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73
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74 try:
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75 # Basic sanity checks
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76 if not os.path.exists(ARGS.input):
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77 logging.error('Input file not found: %s', ARGS.input)
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78
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79 out_dir = os.path.dirname(os.path.abspath(ARGS.output))
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80
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81 if out_dir and not os.path.isdir(out_dir):
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82 try:
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83 os.makedirs(out_dir, exist_ok=True)
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84 logging.info('Created missing output directory: %s', out_dir)
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85 except Exception as e:
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86 logging.exception('Cannot create output directory: %s', out_dir)
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87
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88 model = modelUtils.build_cobra_model_from_csv(ARGS.input)
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89
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90 # Save model in requested format
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91 if ARGS.format == "sbml":
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92 cobra.io.write_sbml_model(model, ARGS.output)
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93 elif ARGS.format == "json":
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94 cobra.io.save_json_model(model, ARGS.output)
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95 elif ARGS.format == "mat":
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96 cobra.io.save_matlab_model(model, ARGS.output)
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97 elif ARGS.format == "yaml":
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98 cobra.io.save_yaml_model(model, ARGS.output)
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99 else:
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100 logging.error('Unknown format requested: %s', ARGS.format)
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101 print(f"ERROR: Unknown format: {ARGS.format}")
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102
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103
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104 logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)
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105
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106 except Exception:
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107 # Log full traceback to the out_log so Galaxy users/admins can see what happened
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108 logging.exception('Unhandled exception in fromCSVtoCOBRA')
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109
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110
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111 if __name__ == '__main__':
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112 main()
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