def test_merge():
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()
ksi1 = KmerSignatureIndex.create(storage, bloomfilters,
bloomfilter_size,
number_hash_functions)
ksi2 = KmerSignatureIndex.create(storage, bloomfilters,
bloomfilter_size,
number_hash_functions)
ksi1.merge_indexes(ksi2)
assert ksi1.lookup(["ATC"]) == {"ATC": bitarray("11" * 2)}
assert ksi1.lookup(["ATC", "ATC", "ATT"]) == {
"ATC": bitarray("11" * 2),
"ATT": bitarray("10" * 2),
}
assert ksi1.lookup(["ATC", "ATC", "ATT", "TTT"]) == {
"ATC": bitarray("11" * 2),
"ATT": bitarray("10" * 2),
"TTT": bitarray("01" * 2),
}
def __init__(self, config=None):
if config is None:
config = DEFAULT_CONFIG
self.config = config
self.storage = get_storage(config)
SampleMetadata.__init__(self, self.storage)
KmerSignatureIndex.__init__(self, self.storage)
self.min_unique_kmers_in_query = (
MIN_UNIQUE_KMERS_IN_QUERY
) ## TODO this can be inferred and set at build time
self.scorer=Scorer(self.num_samples)
def test_lookup1():
bloomfilter_size = 250
number_hash_functions = 3
kmers1 = ["ATC", "ATG", "ATA", "ATT"]
kmers2 = ["ATC", "ATG", "ATA", "TTT"]
bloomfilter1 = BloomFilter(bloomfilter_size, number_hash_functions).update(
convert_query_kmers(kmers1)) # canonical
bloomfilter2 = BloomFilter(bloomfilter_size, number_hash_functions).update(
convert_query_kmers(kmers2))
bloomfilters = [bloomfilter1.bitarray, bloomfilter2.bitarray]
for storage in get_storages():
storage.delete_all()
KmerSignatureIndex.create(storage, bloomfilters, bloomfilter_size,
number_hash_functions)
ksi = KmerSignatureIndex(storage)
assert ksi.lookup(["ATC"]) == {"ATC": bitarray("11")}
print(ksi.lookup(["ATC", "ATC", "ATT"]))
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 build(cls, config, bloomfilters, samples):
storage = get_storage(config)
validate_build_params(bloomfilters, samples)
logger.debug("Insert sample metadata")
sm = SampleMetadata(storage).add_samples(samples)
logger.debug("Create signature index")
ksi = KmerSignatureIndex.create(
storage,
bloomfilters,
config["m"],
config["h"],
config.get("low_mem_build", False),
)
storage.close() ## Need to delete LOCK files before re init
return cls(config)