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

Uploaded

541:fa93040a75af

import pickle as pk
import pandas as pd

from typing import Optional, List, Dict

import utils.general_utils as utils
import utils.reaction_parsing as reactionUtils

########################## argparse ##########################################
ARGS :argparse.Namespace
def process_args(args:List[str] = None) -> argparse.Namespace:
    """

    
    parser.add_argument("-rl", "--model_upload", type = str,
        help = "path to input file containing the reactions")

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

542:fcdbc81feb45

import pickle as pk
import pandas as pd

from typing import Optional, List, Dict

try:
    from .utils import general_utils as utils
    from .utils import reaction_parsing as reactionUtils
except:
    import utils.general_utils as utils
    import utils.reaction_parsing as reactionUtils

########################## argparse ##########################################
ARGS :argparse.Namespace
def process_args(args:List[str] = None) -> argparse.Namespace:
    """

    
    parser.add_argument("-rl", "--model_upload", type = str,
        help = "path to input file containing the reactions")

    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('-ol', '--out_log', 
                        help = "Output log")    
    parser.add_argument('-id', '--input',
                        type = str,
                        required = True,