mzmine2ionlist.py

import pandas as pd
import argparse


def gen_nominal_decimal(mz):
    nominal = int(mz)
    decimal = mz-nominal
    return nominal, decimal


def parse_arguments():
    """
    Parse command-line arguments using argparse.
    """
    parser = argparse.ArgumentParser(description="Convert MZmine output quant table to ion list for NegMDF.")
    
    # 输入文件参数
    parser.add_argument(
        "-i", "--input",
        type=str,
        required=True,
        help="Path to the input quant table (CSV format) generated by MZmine."
    )
    
    # 输出文件参数
    parser.add_argument(
        "-o", "--output",
        type=str,
        required=True,
        help="Path to save the output ion list (CSV format)."
    )
    
    return parser.parse_args()


if __name__ == '__main__':
    args = parse_arguments()
    mzmine_df = pd.read_csv(args.input)
    mzmine_df_target_col = ["row ID","row retention time", "row m/z"]
    ion_list_df = pd.DataFrame()
    ion_list_df[["id", "rt", "mz"]] = mzmine_df[mzmine_df_target_col]
    ion_list_df[["integer", "decimal"]] = ion_list_df["mz"].apply(gen_nominal_decimal).apply(pd.Series)
    ion_list_df["integer"] = ion_list_df["integer"].astype(int)
    ion_list_df.to_csv(args.output, index=False)