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1 import os
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2 import csv
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3 import cobra
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4 import pickle
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5 import argparse
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6 import pandas as pd
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7 import utils.general_utils as utils
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8 from typing import Optional, Tuple, Union, List, Dict
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9 import logging
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10 import utils.rule_parsing as rulesUtils
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11 import utils.reaction_parsing as reactionUtils
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12 import utils.model_utils as modelUtils
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13
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14 ARGS : argparse.Namespace
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15 def process_args(args: List[str] = None) -> argparse.Namespace:
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453
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16 parser = argparse.ArgumentParser(
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17 usage="%(prog)s [options]",
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18 description="Convert a tabular/CSV file to a COBRA model"
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19 )
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20
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21
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22 parser.add_argument("--out_log", type=str, required=True,
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23 help="Output log file")
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24
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25
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26 parser.add_argument("--input", type=str, required=True,
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27 help="Input tabular file (CSV/TSV)")
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28
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29
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30 parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
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31 help="Model format (SBML, JSON, MATLAB, YAML)")
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32
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33
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34 parser.add_argument("--output", type=str, required=True,
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35 help="Output model file path")
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36
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37
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38 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
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39 help="Tool directory (passed from Galaxy as $__tool_directory__)")
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40
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41
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42 return parser.parse_args(args)
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43
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453
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44
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451
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45 ###############################- ENTRY POINT -################################
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46
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47 def main(args: List[str] = None) -> None:
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451
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48 global ARGS
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49 ARGS = process_args(args)
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50
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51 # configure logging to the requested log file (overwrite each run)
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52 logging.basicConfig(filename=ARGS.out_log,
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53 level=logging.DEBUG,
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54 format='%(asctime)s %(levelname)s: %(message)s',
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55 filemode='w')
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56
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57 logging.info('Starting fromCSVtoCOBRA tool')
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58 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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59
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60 try:
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61 # Basic sanity checks
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62 if not os.path.exists(ARGS.input):
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63 logging.error('Input file not found: %s', ARGS.input)
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64
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65 out_dir = os.path.dirname(os.path.abspath(ARGS.output))
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455
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66
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67 if out_dir and not os.path.isdir(out_dir):
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68 try:
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69 os.makedirs(out_dir, exist_ok=True)
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70 logging.info('Created missing output directory: %s', out_dir)
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71 except Exception as e:
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72 logging.exception('Cannot create output directory: %s', out_dir)
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73
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74 model = modelUtils.build_cobra_model_from_csv(ARGS.input)
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75
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76 # Save model in requested format
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77 if ARGS.format == "sbml":
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78 cobra.io.write_sbml_model(model, ARGS.output)
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79 elif ARGS.format == "json":
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80 cobra.io.save_json_model(model, ARGS.output)
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81 elif ARGS.format == "mat":
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82 cobra.io.save_matlab_model(model, ARGS.output)
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83 elif ARGS.format == "yaml":
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84 cobra.io.save_yaml_model(model, ARGS.output)
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85 else:
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86 logging.error('Unknown format requested: %s', ARGS.format)
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87 print(f"ERROR: Unknown format: {ARGS.format}")
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88
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89
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90 logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)
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91
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92 except Exception:
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93 # Log full traceback to the out_log so Galaxy users/admins can see what happened
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94 logging.exception('Unhandled exception in fromCSVtoCOBRA')
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451
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95
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96
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97 if __name__ == '__main__':
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98 main()
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