Extract an HMM profile from a set

pull_hmm.py

#!/usr/bin/env python3

import argparse
import os
import sys
from typing import IO


def _main(accession: str, source: IO, destination: IO) -> int:
    if not accession:
        print("error: accession cannot be empty", file=sys.stderr)
        return 2

    profile = []
    correct_profile = False
    for line in source:
        profile.append(line)
        if line.startswith("//"):
            if correct_profile:
                break
            profile.clear()
        if (line.startswith("NAME ") or line.startswith("ACC ")) and line.split()[-1] == accession:
            correct_profile = True

    if not profile:
        print(f"error: no profile found with accession or name of: {accession}", file=sys.stderr)
        return 3
    if not profile[-1].startswith("//"):
        print("error: input ended abruptly", file=sys.stderr)
        return 4

    for line in profile:
        destination.write(line)

    return 0


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument("identifier", type=str, help="The name/accession of the profile to extract")
    parser.add_argument("source", type=argparse.FileType('r'), default=sys.stdin,
                        help="The full set of HMMer profiles")
    parser.add_argument("destination", nargs="?", type=argparse.FileType('w'), default=sys.stdout,
                        help="The output location (default: stdout)")
    args = parser.parse_args()
    sys.exit(_main(args.identifier, args.source, args.destination))