comparison COBRAxy/fromCSVtoCOBRA_beta.py @ 456:a6e45049c1b9 draft

Uploaded

455:4e2bc80764b6

import os
import csv
import cobra
import pickle
import argparse
import pandas as pd
import utils.general_utils as utils
from typing import Optional, Tuple, Union, List, Dict
import logging
import utils.rule_parsing  as rulesUtils
import utils.reaction_parsing as reactionUtils
import utils.model_utils as modelUtils

ARGS : argparse.Namespace
def process_args(args: List[str] = None) -> argparse.Namespace:
    parser = argparse.ArgumentParser(
    usage="%(prog)s [options]",
    description="Convert a tabular/CSV file to a COBRA model"
    )

###############################- ENTRY POINT -################################

def main(args: List[str] = None) -> None:
    global ARGS
    ARGS = process_args(args)

    # configure logging to the requested log file (overwrite each run)
    logging.basicConfig(filename=ARGS.out_log,

456:a6e45049c1b9

"""
Convert a tabular (CSV/TSV/Tabular) description of a COBRA model into a COBRA file.

Supported output formats: SBML, JSON, MATLAB (.mat), YAML.
The script logs to a user-provided file for easier debugging in Galaxy.
"""

import os
import cobra
import argparse
from typing import List
import logging
import utils.model_utils as modelUtils

ARGS : argparse.Namespace
def process_args(args: List[str] = None) -> argparse.Namespace:
    """
    Parse command-line arguments for the CSV-to-COBRA conversion tool.

    Returns:
        argparse.Namespace: Parsed arguments.
    """
    parser = argparse.ArgumentParser(
    usage="%(prog)s [options]",
    description="Convert a tabular/CSV file to a COBRA model"
    )

###############################- ENTRY POINT -################################

def main(args: List[str] = None) -> None:
    """
    Entry point: parse arguments, build the COBRA model from a CSV/TSV file,
    and save it in the requested format.

    Returns:
        None
    """
    global ARGS
    ARGS = process_args(args)

    # configure logging to the requested log file (overwrite each run)
    logging.basicConfig(filename=ARGS.out_log,