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542
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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
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14 try:
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15 from .utils import model_utils as modelUtils
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16 from .utils import general_utils as utils
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17 except:
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18 import utils.model_utils as modelUtils
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19 import utils.general_utils as utils
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20
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21 ARGS : argparse.Namespace
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22 def process_args(args: List[str] = None) -> argparse.Namespace:
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23 """
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24 Parse command-line arguments for the CSV-to-COBRA conversion tool.
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25
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26 Returns:
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27 argparse.Namespace: Parsed arguments.
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28 """
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29 parser = argparse.ArgumentParser(
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30 usage="%(prog)s [options]",
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31 description="Convert a tabular/CSV file to a COBRA model"
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32 )
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33
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34
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35 parser.add_argument("--out_log", type=str, required=True,
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36 help="Output log file")
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37
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38
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39 parser.add_argument("--input", type=str, required=True,
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40 help="Input tabular file (CSV/TSV)")
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41
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42
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43 parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
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44 help="Model format (SBML, JSON, MATLAB, YAML)")
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45
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46
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47 parser.add_argument("--output", type=str, required=True,
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48 help="Output model file path")
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49
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50 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(os.path.abspath(__file__)),
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51 help="Tool directory (default: auto-detected package location)")
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52
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53
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54 return parser.parse_args(args)
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55
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56
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57 ###############################- ENTRY POINT -################################
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58
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59 def main(args: List[str] = None) -> None:
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60 """
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61 Entry point: parse arguments, build the COBRA model from a CSV/TSV file,
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62 and save it in the requested format.
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63
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64 Returns:
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65 None
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66 """
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67 global ARGS
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68 ARGS = process_args(args)
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69
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70 # configure logging to the requested log file (overwrite each run)
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71 logging.basicConfig(filename=ARGS.out_log,
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72 level=logging.DEBUG,
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73 format='%(asctime)s %(levelname)s: %(message)s',
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74 filemode='w')
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75
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76 logging.info('Starting fromCSVtoCOBRA tool')
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77 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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78
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79 try:
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80 # Basic sanity checks
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81 if not os.path.exists(ARGS.input):
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82 logging.error('Input file not found: %s', ARGS.input)
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83
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84 out_dir = os.path.dirname(os.path.abspath(ARGS.output))
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85
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86 if out_dir and not os.path.isdir(out_dir):
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87 try:
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88 os.makedirs(out_dir, exist_ok=True)
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89 logging.info('Created missing output directory: %s', out_dir)
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90 except Exception as e:
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91 logging.exception('Cannot create output directory: %s', out_dir)
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92
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93 model = modelUtils.build_cobra_model_from_csv(ARGS.input)
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94
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95
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96 logging.info('Created model with name: %s (ID: %s)', model.name, model.id)
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97
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98 # Save model in requested format - Galaxy handles the filename
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99 if ARGS.format == "sbml":
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100 cobra.io.write_sbml_model(model, ARGS.output)
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101 elif ARGS.format == "json":
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102 cobra.io.save_json_model(model, ARGS.output)
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103 elif ARGS.format == "mat":
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104 cobra.io.save_matlab_model(model, ARGS.output)
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105 elif ARGS.format == "yaml":
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106 cobra.io.save_yaml_model(model, ARGS.output)
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107 else:
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108 logging.error('Unknown format requested: %s', ARGS.format)
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109 raise ValueError(f"Unknown format: {ARGS.format}")
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110
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111
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112 logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)
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113 print(f"Model created successfully in {ARGS.format.upper()} format")
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114
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115 except Exception as e:
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116 # Log full traceback to the out_log so Galaxy users/admins can see what happened
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117 logging.exception('Unhandled exception in fromCSVtoCOBRA')
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118 print(f"ERROR: {str(e)}")
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119 raise
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120
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121
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122 if __name__ == '__main__':
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123 main()
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