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()
def test_merge():
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)
bigsi1 = BIGSI.build(CONFIGS[0], [bloom1], ["a"])
bigsi2 = BIGSI.build(CONFIGS[1], [bloom2], ["b"])
bigsic = BIGSI.build(CONFIGS[2], [bloom1, bloom2], ["a", "b"])
bigsi1.merge(bigsi2)
assert bigsi1.search("ATACACAAT", 0.5) == bigsic.search("ATACACAAT", 0.5)
bigsi1.delete()
bigsi2.delete()
bigsic.delete()
def test_insert():
for config in CONFIGS:
get_storage(config).delete_all()
bloomfilters = [BIGSI.bloom(config, ["ATC", "ATA"])]
samples = ["1"]
bigsi = BIGSI.build(config, bloomfilters, samples)
bloomfilter_2 = BIGSI.bloom(config, ["ATC", "ATT"])
bigsi.insert(bloomfilter_2, "2")
assert bigsi.kmer_size == 3
assert bigsi.bloomfilter_size == 1000
assert bigsi.num_hashes == 3
assert bigsi.num_samples == 2
assert bigsi.lookup(["ATC", "ATA", "ATT"]) == {
"ATC": bitarray("11"),
"ATA": bitarray("10"),
"ATT": bitarray("01"),
}
assert bigsi.colour_to_sample(0) == "1"
assert bigsi.sample_to_colour("1") == 0
assert bigsi.colour_to_sample(1) == "2"
assert bigsi.sample_to_colour("2") == 1
bigsi.delete()
def test_exact_search():
config = CONFIGS[0]
kmers_1 = seq_to_kmers("ATACACAAT", config["k"])
kmers_2 = seq_to_kmers("ACAGAGAAC", config["k"])
bloom1 = BIGSI.bloom(config, kmers_1)
bloom2 = BIGSI.bloom(config, kmers_2)
for config in CONFIGS:
get_storage(config).delete_all()
bigsi = BIGSI.build(config, [bloom1, bloom2], ["a", "b"])
assert bigsi.search("ATACACAAT")[0] == {
"percent_kmers_found": 100,
"num_kmers": 6,
"num_kmers_found": 6,
"sample_name": "a",
}
assert bigsi.search("ACAGAGAAC")[0] == {
"percent_kmers_found": 100,
"num_kmers": 6,
"num_kmers_found": 6,
"sample_name": "b",
}
assert bigsi.search("ACAGTTAAC") == []
bigsi.delete()
def test_create():
for config in CONFIGS:
get_storage(config).delete_all()
bloomfilters = [BIGSI.bloom(config, ["ATC", "ATA"])]
samples = ["1"]
bigsi = BIGSI.build(config, bloomfilters, samples)
assert bigsi.kmer_size == 3
assert bigsi.bloomfilter_size == 1000
assert bigsi.num_hashes == 3
assert bigsi.num_samples == 1
assert bigsi.lookup("ATC") == {"ATC": bitarray("1")}
assert bigsi.colour_to_sample(0) == "1"
assert bigsi.sample_to_colour("1") == 0
bigsi.delete()
def test_unique_sample_names():
for config in CONFIGS:
get_storage(config).delete_all()
bloom = BIGSI.bloom(config, ["ATC", "ATA"])
bigsi = BIGSI.build(config, [bloom], ["1"])
with pytest.raises(ValueError):
bigsi.insert(bloom, "1")
assert bigsi.num_samples == 1
assert bigsi.lookup(["ATC", "ATA", "ATT"]) == {
"ATC": bitarray("1"),
"ATA": bitarray("1"),
"ATT": bitarray("0"),
}
bigsi.delete()
