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 test_bloomfilter_updated_success(len_bloom_filter, num_hash_functions, len_kmer, num_kmers):
kmers = _generate_random_kmers(len_kmer, num_kmers)
hashes = _generate_kmer_hashes(kmers, len_bloom_filter, num_hash_functions)
expected = bitarray("0" * len_bloom_filter)
for h in hashes:
expected[h] = True
bloom_filter = BloomFilter(m=len_bloom_filter, h=num_hash_functions)
bloom_filter.update(kmers)
assert bloom_filter.bitarray == expected
def test_bloomfilters_updated_with_same_kmers(len_bloom_filter, num_hash_functions, len_kmer, num_kmers):
kmers = _generate_random_kmers(len_kmer, num_kmers)
bloom_filter1 = BloomFilter(m=len_bloom_filter, h=num_hash_functions)
bloom_filter1.update(kmers)
bloom_filter2 = BloomFilter(m=len_bloom_filter, h=num_hash_functions)
bloom_filter2.update(kmers)
assert bloom_filter1.bitarray == bloom_filter2.bitarray
def test_create_bloom():
for i in range(3):
kmers1 = ["ATT", "ATC"]
bloomfilter1 = BloomFilter(m=25, h=3)
bloomfilter1.update(kmers1)
kmers2 = ["ATT", "ATT"]
bloomfilter2 = BloomFilter(m=25, h=3)
bloomfilter2.update(kmers2)
assert bloomfilter1.bitarray != bloomfilter2.bitarray
def test_bloomfilters_updated_with_different_kmers(len_bloom_filter, num_hash_functions, len_kmer, num_kmers):
kmers1 = _generate_random_kmers(len_kmer, num_kmers)
hashes1 = _generate_kmer_hashes(kmers1, len_bloom_filter, num_hash_functions)
kmers2 = _generate_random_kmers(len_kmer, num_kmers)
hashes2 = _generate_kmer_hashes(kmers2, len_bloom_filter, num_hash_functions)
assume(hashes1 != hashes2)
bloom_filter1 = BloomFilter(m=len_bloom_filter, h=num_hash_functions)
bloom_filter1.update(kmers1)
bloom_filter2 = BloomFilter(m=len_bloom_filter, h=num_hash_functions)
bloom_filter2.update(kmers2)
assert bloom_filter1.bitarray != bloom_filter2.bitarray
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
def test_bloomfilter_created_with_initialisation(len_bloom_filter, num_hash_functions):
bloom_filter = BloomFilter(m=len_bloom_filter, h=num_hash_functions)
assert bloom_filter.bitarray == bitarray("0" * len_bloom_filter)