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

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541:fa93040a75af

- Build a COBRA model from a tabular CSV
- Run FVA to initialize bounds, then scale per-sample based on RAS values
- Save bounds per sample and optionally export updated models in chosen formats
"""
import argparse
import utils.general_utils as utils
from typing import Optional, Dict, Set, List, Tuple, Union
import os
import numpy as np
import pandas as pd
import cobra
from cobra import Model
import sys
from joblib import Parallel, delayed, cpu_count
import utils.model_utils as modelUtils

################################# process args ###############################
def process_args(args :List[str] = None) -> argparse.Namespace:
    """
    Processes command-line arguments.

    parser.add_argument('-ol', '--out_log', 
                        help = "Output log")
    
    parser.add_argument('-td', '--tool_dir',
                        type = str,
                        required = True,
                        help = 'your tool directory')
    
    parser.add_argument('-ir', '--input_ras',
                        type=str,
                        required = False,
                        help = 'input ras')

542:fcdbc81feb45

- Build a COBRA model from a tabular CSV
- Run FVA to initialize bounds, then scale per-sample based on RAS values
- Save bounds per sample and optionally export updated models in chosen formats
"""
import argparse
from typing import Optional, Dict, Set, List, Tuple, Union
import os
import numpy as np
import pandas as pd
import cobra
from cobra import Model
import sys
from joblib import Parallel, delayed, cpu_count

try:
    from .utils import general_utils as utils
    from .utils import model_utils as modelUtils
except:
    import utils.general_utils as utils
    import utils.model_utils as modelUtils

################################# process args ###############################
def process_args(args :List[str] = None) -> argparse.Namespace:
    """
    Processes command-line arguments.

    parser.add_argument('-ol', '--out_log', 
                        help = "Output log")
    
    parser.add_argument('-td', '--tool_dir',
                        type = str,
                        default = os.path.dirname(os.path.abspath(__file__)),
                        help = 'your tool directory (default: auto-detected package location)')
    
    parser.add_argument('-ir', '--input_ras',
                        type=str,
                        required = False,
                        help = 'input ras')