comparison COBRAxy/ras_to_bounds.py @ 147:3fca9b568faf draft

Uploaded

146:88cf4543e210

import sys
import csv
from joblib import Parallel, delayed, cpu_count

################################# process args ###############################
def process_args(args :List[str]) -> argparse.Namespace:
    """
    Processes command-line arguments.

    Args:
        args (list): List of command-line arguments.

                        help = 'ras selector')

    parser.add_argument('-cc', '--cell_class',
                    type = str,
                    help = 'output of cell class')
    
    
    ARGS = parser.parse_args()
    return ARGS

########################### warning ###########################################
def warning(s :str) -> None:
    """

    pass



############################# main ###########################################
def main() -> None:
    """
    Initializes everything and sets the program in motion based on the fronted input arguments.

    Returns:
        None

    if not os.path.exists('ras_to_bounds'):
        os.makedirs('ras_to_bounds')


    global ARGS
    ARGS = process_args(sys.argv)

    ARGS.output_folder = 'ras_to_bounds/'

    if(ARGS.ras_selector == True):
        ras_file_list = ARGS.input_ras.split(",")
        ras_file_names = ARGS.name.split(",")
        if len(ras_file_names) != len(set(ras_file_names)):

        ARGS.medium_selector = ARGS.medium_selector.replace("_", " ")
        medium = df_mediums[[ARGS.medium_selector]]
        medium = medium[ARGS.medium_selector].to_dict()

    if(ARGS.ras_selector == True):
        generate_bounds(model, medium, ras = ras_combined, output_folder=ARGS.output_folder)
        class_assignments.to_csv(ARGS.cell_class, sep = '\t', index = False)
    else:
        generate_bounds(model, medium, output_folder=ARGS.output_folder)

    pass
        
##############################################################################
if __name__ == "__main__":

147:3fca9b568faf

import sys
import csv
from joblib import Parallel, delayed, cpu_count

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

    Args:
        args (list): List of command-line arguments.

                        help = 'ras selector')

    parser.add_argument('-cc', '--cell_class',
                    type = str,
                    help = 'output of cell class')
    parser.add_argument(
        '-idop', '--output_path', 
        type = str,
        default='ras_to_bounds/',
        help = 'output path for maps')
    
    
    ARGS = parser.parse_args(args)
    return ARGS

########################### warning ###########################################
def warning(s :str) -> None:
    """

    pass



############################# main ###########################################
def main(args:List[str] = None) -> None:
    """
    Initializes everything and sets the program in motion based on the fronted input arguments.

    Returns:
        None

    if not os.path.exists('ras_to_bounds'):
        os.makedirs('ras_to_bounds')


    global ARGS
    ARGS = process_args(args)

    if(ARGS.ras_selector == True):
        ras_file_list = ARGS.input_ras.split(",")
        ras_file_names = ARGS.name.split(",")
        if len(ras_file_names) != len(set(ras_file_names)):

        ARGS.medium_selector = ARGS.medium_selector.replace("_", " ")
        medium = df_mediums[[ARGS.medium_selector]]
        medium = medium[ARGS.medium_selector].to_dict()

    if(ARGS.ras_selector == True):
        generate_bounds(model, medium, ras = ras_combined, output_folder=ARGS.output_path)
        class_assignments.to_csv(ARGS.cell_class, sep = '\t', index = False)
    else:
        generate_bounds(model, medium, output_folder=ARGS.output_path)

    pass
        
##############################################################################
if __name__ == "__main__":