from docker_run import run_command

def run_hmmsearch(sequences_file: str, hmm_file: str, output_file: str, out_type = "out"):
    if out_type == "out":
        run_command(f"hmmsearch`{hmm_file}`{sequences_file}`>`{output_file}", sep = "`")
    elif out_type == "tsv":
        run_command(f"hmmsearch`--tblout`{output_file}`{hmm_file}`{sequences_file}", sep = "`")
    elif out_type == "pfam":
        run_command(f"hmmsearch`--pfamtblout`{output_file}`{hmm_file}`{sequences_file}", sep = "`")