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comparison COBRAxy/src/importMetabolicModel.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
10 import os 10 import os
11 import csv 11 import csv
12 import cobra 12 import cobra
13 import argparse 13 import argparse
14 import pandas as pd 14 import pandas as pd
15 import utils.general_utils as utils 15 try:
16 from .utils import general_utils as utils
17 from .utils import model_utils as modelUtils
18 except:
19 import utils.general_utils as utils
20 import utils.model_utils as modelUtils
16 from typing import Optional, Tuple, List 21 from typing import Optional, Tuple, List
17 import utils.model_utils as modelUtils
18 import logging 22 import logging
19 from pathlib import Path 23 from pathlib import Path
20 24
21 25
22 ARGS : argparse.Namespace 26 ARGS : argparse.Namespace
38 parser.add_argument("--input", type=str, 42 parser.add_argument("--input", type=str,
39 help="Custom model file (JSON, XML, MAT, YAML)") 43 help="Custom model file (JSON, XML, MAT, YAML)")
40 parser.add_argument("--name", nargs='*', required=True, 44 parser.add_argument("--name", nargs='*', required=True,
41 help="Model name (default or custom)") 45 help="Model name (default or custom)")
42 46
43 parser.add_argument("--medium_selector", type=str, required=True, 47 parser.add_argument("--medium_selector", type=str, default="Default",
44 help="Medium selection option") 48 help="Medium selection option")
45 49
46 parser.add_argument("--gene_format", type=str, default="Default", 50 parser.add_argument("--gene_format", type=str, default="Default",
47 help="Gene nomenclature format: Default (original), ENSNG, HGNC_SYMBOL, HGNC_ID, ENTREZ") 51 help="Gene nomenclature format: Default (original), ENSNG, HGNC_SYMBOL, HGNC_ID, ENTREZ")
48 52
49 parser.add_argument("--out_tabular", type=str, 53 parser.add_argument("--out_tabular", type=str,
50 help="Output file for the merged dataset (CSV or XLSX)") 54 help="Output file for the merged dataset (CSV or XLSX)")
51 55
52 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__), 56 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(os.path.abspath(__file__)),
53 help="Tool directory (passed from Galaxy as $__tool_directory__)") 57 help="Tool directory (default: auto-detected package location)")
54 58
55 59
56 return parser.parse_args(args) 60 return parser.parse_args(args)
57 61
58 ################################- INPUT DATA LOADING -################################ 62 ################################- INPUT DATA LOADING -################################