def _q_start(query_seq, q_seq):
    """
    returns the starting pytyon string index of query alignment (q_seq) in the query_sequence (query_seq)

    :param query_seq: string full query sequence
    :param q_seq: string alignment sequence (may contain gaps as "-")
    :return:
    :example:
    >>_q_start(query_seq = "ATGATG", q_seq = "ATG")
    0
    >>_q_start(query_seq = "ATGATG", q_seq = "GATG")
    2
    >>_q_start(query_seq="ATGATG", q_seq="GA-TG")
    2
    """
    q_seq = q_seq.replace("-", "") # remove gaps to get index for original sequence
    q_start = query_seq.find(q_seq)
    return(q_start)