def filter_rep_set(inF, otuSet):
    """
    Parse the rep set file and remove all sequences not associated with unique
    OTUs.

    :@type inF: file
    :@param inF: The representative sequence set

    :@rtype: list
    :@return: The set of sequences associated with unique OTUs
    """
    seqs = []
    for record in SeqIO.parse(inF, "fasta"):
        if record.id in otuSet:
            seqs.append(record)
    return seqs