#!/usr/bin/env python3

import argparse
import csv
import sys


def parse_args():
    parser = argparse.ArgumentParser()
    parser.add_argument("modified_bases_tsv")
    return parser.parse_args()


def infer_codes(modified_bases_tsv):
    codes = []
    seen = set()

    with open(modified_bases_tsv, newline="") as handle:
        reader = csv.DictReader(handle, delimiter="\t")
        for row in reader:
            primary_base = row.get("primary_base", "").strip()
            mod_code = row.get("mod_code", "").strip()
            if not primary_base or not mod_code:
                continue

            code = f"{primary_base}:{mod_code}"
            if code not in seen:
                seen.add(code)
                codes.append(code)

    return codes


def main():
    args = parse_args()
    codes = infer_codes(args.modified_bases_tsv)
    if not codes:
        sys.stderr.write("Failed to infer modified base codes from modified_bases.tsv\n")
        raise SystemExit(1)

    sys.stdout.write(",".join(codes) + "\n")


if __name__ == "__main__":
    main()