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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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16 """
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17 Parse command-line arguments for CustomDataGenerator.
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18 """
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19
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20 parser = argparse.ArgumentParser(
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21 usage="%(prog)s [options]",
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22 description="Generate custom data from a given model"
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23 )
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24
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25 parser.add_argument("--out_log", type=str, required=True,
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26 help="Output log file")
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27
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28 parser.add_argument("--input", type=str,
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29 help="Input tabular file")
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30
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31 parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
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32 help="Model format (SBML, JSON, MATLAB, YAML)")
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33
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34 parser.add_argument("--output", type=str,
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35 help="Output model file")
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36
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37 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
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38 help="Tool directory (passed from Galaxy as $__tool_directory__)")
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39
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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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44 ###############################- ENTRY POINT -################################
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45 def main(args:List[str] = None) -> None:
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46 """
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47 Initializes everything and sets the program in motion based on the fronted input arguments.
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48
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49 Returns:
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50 None
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51 """
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52 # get args from frontend (related xml)
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53 global ARGS
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54 ARGS = process_args(args)
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55
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56 model = modelUtils.build_cobra_model_from_csv(ARGS.model_upload)
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57
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58
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59 if ARGS.format == "sbml":
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60 cobra.io.write_sbml_model(model, ARGS.output)
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61 elif ARGS.format == "json":
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62 cobra.io.save_json_model(model, ARGS.output)
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63 elif ARGS.format == "mat":
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64 cobra.io.save_matlab_model(model, ARGS.output)
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65 elif ARGS.format == "yaml":
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66 cobra.io.save_yaml_model(model, ARGS.output)
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67
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68 if __name__ == '__main__':
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69 main() |
