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

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author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
parents 2fb97466e404
children 01147e83f43c
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541:fa93040a75af 542:fcdbc81feb45
9 Sampling algorithms supported: OPTGP and CBS. Outputs include flux samples 9 Sampling algorithms supported: OPTGP and CBS. Outputs include flux samples
10 and optional analyses (pFBA, FVA, sensitivity), saved as tabular files. 10 and optional analyses (pFBA, FVA, sensitivity), saved as tabular files.
11 """ 11 """
12 12
13 import argparse 13 import argparse
14 import utils.general_utils as utils
15 from typing import List 14 from typing import List
16 import os 15 import os
17 import pandas as pd 16 import pandas as pd
18 import numpy as np 17 import numpy as np
19 import cobra 18 import cobra
20 import utils.CBS_backend as CBS_backend
21 from joblib import Parallel, delayed, cpu_count 19 from joblib import Parallel, delayed, cpu_count
22 from cobra.sampling import OptGPSampler 20 from cobra.sampling import OptGPSampler
23 import sys 21 import sys
24 import utils.model_utils as model_utils 22
23 try:
24 from .utils import general_utils as utils
25 from .utils import CBS_backend
26 from .utils import model_utils
27 except:
28 import utils.general_utils as utils
29 import utils.CBS_backend as CBS_backend
30 import utils.model_utils as model_utils
25 31
26 32
27 ################################# process args ############################### 33 ################################# process args ###############################
28 def process_args(args: List[str] = None) -> argparse.Namespace: 34 def process_args(args: List[str] = None) -> argparse.Namespace:
29 """ 35 """
54 parser.add_argument('-ol', '--out_log', 60 parser.add_argument('-ol', '--out_log',
55 help="Output log") 61 help="Output log")
56 62
57 parser.add_argument('-td', '--tool_dir', 63 parser.add_argument('-td', '--tool_dir',
58 type=str, 64 type=str,
59 required=True, 65 default=os.path.dirname(os.path.abspath(__file__)),
60 help='your tool directory') 66 help='your tool directory (default: auto-detected package location)')
61 67
62 parser.add_argument('-in', '--input', 68 parser.add_argument('-in', '--input',
63 required=True, 69 required=True,
64 type=str, 70 type=str,
65 help='input bounds files or complete model files') 71 help='input bounds files or complete model files')