Mercurial > repos > bimib > cobraxy

comparison COBRAxy/src/exportMetabolicModel.py @ 542:fcdbc81feb45 draft

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author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
parents 7d5b35c715e8
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541:fa93040a75af 542:fcdbc81feb45
8 import os 8 import os
9 import cobra 9 import cobra
10 import argparse 10 import argparse
11 from typing import List 11 from typing import List
12 import logging 12 import logging
13 import utils.model_utils as modelUtils 13
14 try:
15 from .utils import model_utils as modelUtils
16 from .utils import general_utils as utils
17 except:
18 import utils.model_utils as modelUtils
19 import utils.general_utils as utils
14 20
15 ARGS : argparse.Namespace 21 ARGS : argparse.Namespace
16 def process_args(args: List[str] = None) -> argparse.Namespace: 22 def process_args(args: List[str] = None) -> argparse.Namespace:
17 """ 23 """
18 Parse command-line arguments for the CSV-to-COBRA conversion tool. 24 Parse command-line arguments for the CSV-to-COBRA conversion tool.
39 45
40 46
41 parser.add_argument("--output", type=str, required=True, 47 parser.add_argument("--output", type=str, required=True,
42 help="Output model file path") 48 help="Output model file path")
43 49
44 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__), 50 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(os.path.abspath(__file__)),
45 help="Tool directory (passed from Galaxy as $__tool_directory__)") 51 help="Tool directory (default: auto-detected package location)")
46 52
47 53
48 return parser.parse_args(args) 54 return parser.parse_args(args)
49 55
50 56