Mercurial > repos > bimib > marea_2_0
changeset 217:438ab7800c85 draft
Uploaded
author | luca_milaz |
---|---|
date | Sat, 06 Jul 2024 09:38:13 +0000 |
parents | da5071684811 |
children | ff46698e0eab |
files | marea_2_0/utils/model_generator.py |
diffstat | 1 files changed, 125 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/marea_2_0/utils/model_generator.py Sat Jul 06 09:38:13 2024 +0000 @@ -0,0 +1,125 @@ +import argparse +import utils.general_utils as utils +from typing import Optional, List +import os +import numpy as np +import pandas as pd +import cobra +from joblib import Parallel, delayed, cpu_count +import sys + +################################# process args ############################### +def process_args(args :List[str]) -> argparse.Namespace: + """ + Processes command-line arguments. + + Args: + args (list): List of command-line arguments. + + Returns: + Namespace: An object containing parsed arguments. + """ + parser = argparse.ArgumentParser(usage = '%(prog)s [options]', + description = 'process some value\'s') + + parser.add_argument( + '-ms', '--model_selector', + type = utils.Model, default = utils.Model.ENGRO2, choices = list(utils.Model.ENGRO2, utils.Model.Custom), + help = 'chose which type of model you want use') + + parser.add_argument("-mo", "--model", type = str, + help = "path to input file with custom rules, if provided") + + parser.add_argument("-mn", "--model_name", type = str, help = "custom mode name") + + 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('-in', '--model', + required = True, + type=str, + help = 'input model') + + + parser.add_argument('-im', '--input_medium', + required = True, + type=str, + help = 'input medium') + + parser.add_argument('-ir', '--input_ras', + required = True, + type=str, + help = 'input ras') + + parser.add_argument('-ot', '--output_type', + type = str, + required = True, + help = 'output type') + + ARGS = parser.parse_args() + return ARGS + +########################### warning ########################################### +def warning(s :str) -> None: + """ + Log a warning message to an output log file and print it to the console. + + Args: + s (str): The warning message to be logged and printed. + + Returns: + None + """ + with open(ARGS.out_log, 'a') as log: + log.write(s + "\n\n") + print(s) + + +def write_to_file(dataset: pd.DataFrame, name: str, keep_index:bool=False)->None: + dataset.to_csv(ARGS.output_folder + name + ".csv", sep = '\t', index = keep_index) + + +def generate_model(cell_name, ras, medium): + # compute FVA + 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('model_generator'): + os.makedirs('model_generator') + + num_processors = cpu_count() + + global ARGS + ARGS = process_args(sys.argv) + + ARGS.output_folder = 'model_generator/' + + ARGS.output_types = ARGS.output_type.split(",") + + ras = pd.read_table(ARGS.input_ras, header=0, sep=r'\s+', index_col = 0).T + ras.replace("None", None, inplace=True) + + #medium has rows cells and columns medium reactions, not common reactions set to None + medium = pd.read_csv(ARGS.input_medium, sep = '\t', header = 0, engine='python', index_col = 0) + + for index, row in ras.iterrows(): #iterate over cells RAS + generate_model(index, row, medium.loc[index]) + + pass + +############################################################################## +if __name__ == "__main__": + main() \ No newline at end of file