def get_index_list(aln_file_clustal):
    """
        Get the index list of the query.

        Args:
            aln_file_clustal (str): Path to the multiple alignment file (clustal format).

        Returns:
            list: List of the index of the query with gaps.
    """
    # First line of this multiple alignment
    with open(aln_file_clustal, "r") as file:
        query_seq = file.readline()[:-1]
        # "non_gap" positions index are saved into a list
        index_list = [i for i, ele in enumerate(query_seq) if ele != "-"]
    return index_list