Convert newer OpenMS feature tables to a format accepted by older GNPS

convert_openms_feature_version.py

#!/usr/bin/env python3

import argparse
import sys


def convert_lines(lines):
    new_lines = []
    for line in lines:
        # check the modifications are necessary in the first place
        if line.startswith("#CONSENSUS") and "row ID" not in line:
            return lines
        if line.lstrip("#").startswith("CONSENSUS"):
            parts = line.split("\t")
            line = "\t".join(parts[:7] + parts[8:])
        new_lines.append(line)
    return new_lines


def main(args):
    lines = convert_lines(args.input.read().splitlines())
    try:
        for line in lines:
            args.output.write(f"{line}\n")
    except BrokenPipeError:
        return 0
    return 0


if __name__ == '__main__':
    parser = argparse.ArgumentParser(
        description=(
            "Removes the 'row ID' column from OpenMS 3.0 feature qualification tables "
            "so that version 28 of GNPS (the webtool version at time of writing) doesn't crash. "
            "This bug is fixed in GNPS 30, so the conversion isn't necessary"
        ),
    )
    parser.add_argument("input", type=argparse.FileType("r+"), help="The file to convert")
    parser.add_argument('-o', '--output-file', dest="output", type=argparse.FileType("w"),
                        default=sys.stdout, help="A file to write the output to, otherwise it is printed to terminal")
    main(parser.parse_args())