def process_one_file(k, a, filename):
    """Return a set of species over thresholds."""
    with open(filename) as f:
        f.readline()
        species = set()
        for line in f:
            tkns = [tkn.strip() for tkn in line.split('\t')]
            abund, _, _, kmers, _, _, _, rank, taxa_name = tkns
            if rank != 'species':
                continue
            if float(abund) >= a and int(kmers) >= k:
                species.add(taxa_name)
    return species