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test_hll.py
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test_hll.py
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import gzip
from tempfile import NamedTemporaryFile
from screed.fasta import fasta_iter
import pytest
from sourmash.hll import HLL
import sourmash_tst_utils as utils
K = 21 # size of kmer
ERR_RATE = 0.01
N_UNIQUE = 3356
TRANSLATE = {'A': 'T', 'C': 'G', 'T': 'A', 'G': 'C'}
def test_hll_add_python():
# test python code to count unique kmers using HyperLogLog.
# use the lower level add() method, which accepts anything,
# and compare to an exact count using collections.Counter
filename = utils.get_test_data('ecoli.genes.fna')
hll = HLL(ERR_RATE, K)
counter = set()
for n, record in enumerate(fasta_iter(open(filename))):
sequence = record['sequence']
seq_len = len(sequence)
for n in range(0, seq_len + 1 - K):
kmer = sequence[n:n + K]
rc = "".join(TRANSLATE[c] for c in kmer[::-1])
hll.add(kmer)
if rc in counter:
kmer = rc
counter.update([kmer])
n_unique = len(counter)
assert n_unique == N_UNIQUE
assert abs(1 - float(hll.cardinality()) / N_UNIQUE) < ERR_RATE
def test_hll_consume_string():
# test rust code to count unique kmers using HyperLogLog,
# using screed to feed each read to the counter.
filename = utils.get_test_data('ecoli.genes.fna')
hll = HLL(ERR_RATE, K)
n_consumed = n = 0
for n, record in enumerate(fasta_iter(open(filename)), 1):
hll.add_sequence(record['sequence'])
assert abs(1 - float(len(hll)) / N_UNIQUE) < ERR_RATE
def test_hll_similarity_containment():
N_UNIQUE_H1 = 500741
N_UNIQUE_H2 = 995845
N_UNIQUE_U = 995845
SIMILARITY = 0.502783
CONTAINMENT_H1 = 1.
CONTAINMENT_H2 = 0.502783
INTERSECTION = 500838
hll1 = HLL(ERR_RATE, K)
hll2 = HLL(ERR_RATE, K)
hllu = HLL(ERR_RATE, K)
filename = utils.get_test_data('genome-s10.fa.gz')
for n, record in enumerate(fasta_iter(gzip.GzipFile(filename))):
sequence = record['sequence']
seq_len = len(sequence)
for n in range(0, seq_len + 1 - K):
kmer = sequence[n:n + K]
hll1.add(kmer)
hllu.add(kmer)
filename = utils.get_test_data('genome-s10+s11.fa.gz')
for n, record in enumerate(fasta_iter(gzip.GzipFile(filename))):
sequence = record['sequence']
seq_len = len(sequence)
for n in range(0, seq_len + 1 - K):
kmer = sequence[n:n + K]
hll2.add(kmer)
hllu.add(kmer)
assert abs(1 - float(hll1.cardinality()) / N_UNIQUE_H1) < ERR_RATE
assert abs(1 - float(hll2.cardinality()) / N_UNIQUE_H2) < ERR_RATE
assert abs(1 - float(hll1.similarity(hll2)) / SIMILARITY) < ERR_RATE
assert abs(1 - float(hll1.containment(hll2)) / CONTAINMENT_H1) < ERR_RATE
assert abs(1 - float(hll2.containment(hll1)) / CONTAINMENT_H2) < ERR_RATE
assert abs(1 - float(hll1.intersection(hll2)) / INTERSECTION) < ERR_RATE
"""
hll1.merge(hll2)
assert abs(1 - float(hllu.similarity(hll1))) < ERR_RATE
assert abs(1 - float(hllu.containment(hll1))) < ERR_RATE
assert abs(1 - float(hllu.containment(hll2))) < ERR_RATE
assert abs(1 - float(hll1.intersection(hllu)) / N_UNIQUE_U) < ERR_RATE
"""
def test_hll_save_load():
filename = utils.get_test_data('ecoli.genes.fna')
hll = HLL(ERR_RATE, K)
n_consumed = n = 0
for n, record in enumerate(fasta_iter(open(filename)), 1):
hll.add_sequence(record['sequence'])
assert abs(1 - float(len(hll)) / N_UNIQUE) < ERR_RATE
with NamedTemporaryFile() as f:
hll.save(f.name)
new_hll = HLL.load(f.name)
assert len(hll) == len(new_hll)