def test_build_chunks():
N = 3
bloomfilter_filepaths = ['bigsi/tests/data/test_kmers.bloom'] * N
sample_names = generate_sample_names(len(bloomfilter_filepaths))
bigsi1 = BIGSI.create(db="./db-bigsi-no-max-mem/",
m=10,
k=9,
h=1,
force=True)
build(bloomfilter_filepaths, sample_names, bigsi1)
bigsi2 = BIGSI.create(db="./db-bigsi-max-mem/", m=10, k=9, h=1, force=True)
build(bloomfilter_filepaths, sample_names, bigsi2,
max_memory=20) # 20bytes
# Reload and test equal
bigsi1 = BIGSI("./db-bigsi-no-max-mem/")
bigsi2 = BIGSI("./db-bigsi-max-mem")
for i in range(10):
assert bigsi1.graph[i] == bigsi2.graph[i]
for k, v in bigsi2.metadata.items():
assert bigsi1.metadata[k] == v
bigsi1.delete_all()
bigsi2.delete_all()
def test_merge():
kmers1 = ['AAAAAAAAA'] * 3
kmers2 = ['AAAAAAAAT'] * 9
bigsi1 = BIGSI.create(db="./db-bigsi1/", m=10, k=9, h=1, force=True)
blooms1 = []
for s in kmers1:
blooms1.append(bigsi1.bloom([s]))
samples1 = [str(i) for i in range(len(kmers1))]
bigsi1.build(blooms1, samples1)
bigsi2 = BIGSI.create(db="./db-bigsi2/", m=10, k=9, h=1, force=True)
blooms2 = []
for s in kmers2:
blooms2.append(bigsi2.bloom([s]))
samples2 = [str(i) for i in range(len(kmers2))]
bigsi2.build(blooms2, samples2)
combined_samples = combine_samples(samples1, samples2)
bigsicombined = BIGSI.create(db="./db-bigsi-c/",
m=10,
k=9,
h=1,
force=True)
bigsicombined = BIGSI(db="./db-bigsi-c/", mode="c")
bigsicombined.build(blooms1 + blooms2, combined_samples)
bigsi1.merge(bigsi2)
bigsi1 = BIGSI(db="./db-bigsi1/")
for i in range(10):
assert bigsi1.graph[i] == bigsicombined.graph[i]
for k, v in bigsicombined.metadata.items():
assert bigsi1.metadata[k] == v
bigsi1.delete_all()
bigsi2.delete_all()
bigsicombined.delete_all()
def test_inexact_search():
for config in CONFIGS:
get_storage(config).delete_all()
config = CONFIGS[0]
kmers_1 = seq_to_kmers("ATACACAAT", config["k"])
kmers_2 = seq_to_kmers("ATACACAAC", config["k"])
bloom1 = BIGSI.bloom(config, kmers_1)
bloom2 = BIGSI.bloom(config, kmers_2)
for config in CONFIGS:
get_storage(config).delete_all()
with pytest.raises(BaseException):
BIGSI(config)
bigsi = BIGSI.build(config, [bloom1, bloom2], ["a", "b"])
assert bigsi.search("ACAGTTAAC", 0.5) == []
assert bigsi.lookup("AAT") == {"AAT": bitarray("10")}
results = bigsi.search("ATACACAAT", 0.5)
assert results[0] == {
"percent_kmers_found": 100.0,
"num_kmers": 6,
"num_kmers_found": 6,
"sample_name": "a",
}
assert (
json.dumps(results[0])
== '{"percent_kmers_found": 100.0, "num_kmers": 6, "num_kmers_found": 6, "sample_name": "a"}'
)
assert results[1] == {
"percent_kmers_found": 83.33,
"num_kmers": 6,
"num_kmers_found": 5,
"sample_name": "b",
}
bigsi.delete()