def test_lookup3():
bloomfilter_size = 250
number_hash_functions = 1
kmers1 = ["ATC", "ATG", "ATA", "ATT"]
kmers2 = ["ATC", "ATG", "ATA", "TTT"]
bloomfilter1 = BloomFilter(bloomfilter_size, number_hash_functions).update(
convert_query_kmers(kmers1))
bloomfilter2 = BloomFilter(bloomfilter_size, number_hash_functions).update(
convert_query_kmers(kmers2))
bloomfilters = [bloomfilter1, bloomfilter2]
for storage in get_storages():
storage.delete_all()
ksi = KmerSignatureIndex.create(storage, bloomfilters,
bloomfilter_size,
number_hash_functions)
assert ksi.lookup(["ATC"]) == {"ATC": bitarray("11")}
assert ksi.lookup(["ATC", "ATC", "ATT"]) == {
"ATC": bitarray("11"),
"ATT": bitarray("10"),
}
assert ksi.lookup(["ATC", "ATC", "ATT", "TTT"]) == {
"ATC": bitarray("11"),
"ATT": bitarray("10"),
"TTT": bitarray("01"),
}
def bloom(cls, config, kmers):
kmers = convert_query_kmers(kmers) ## Convert to canonical kmers
bloomfilter = BloomFilter(m=config["m"], h=config["h"])
bloomfilter.update(kmers)
return bloomfilter.bitarray