1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
|
"""Benchmarking the cfaidx module. Usage::
pytest benchmark/faidx_bench.py
"""
import os
import pysam
from TestUtils import BAM_DATADIR
def iterate_over_fastx(fn, persist=True):
return len(list(pysam.FastxFile(fn, persist=persist)))
def iterate_over_fastx_as_file(fn):
with open(fn) as inf:
return len(inf.read())
def test_fasta_iteration_short_sequences(benchmark):
result = benchmark(iterate_over_fastx, os.path.join(
BAM_DATADIR, "faidx_ex1.fa"))
assert result == 3270
def test_fasta_iteration_long_sequences(benchmark):
result = benchmark(iterate_over_fastx, os.path.join(BAM_DATADIR, "ex1.fa"))
assert result == 2
def test_fasta_iteration_short_sequences_without_persistence(benchmark):
result = benchmark(iterate_over_fastx, os.path.join(
BAM_DATADIR, "faidx_ex1.fa"), persist=False)
assert result == 3270
def test_fasta_iteration_long_sequences_without_persistence(benchmark):
result = benchmark(iterate_over_fastx, os.path.join(
BAM_DATADIR, "ex1.fa"), persist=False)
assert result == 2
def test_fasta_iteration_short_sequences_as_file(benchmark):
result = benchmark(iterate_over_fastx_as_file,
os.path.join(BAM_DATADIR, "faidx_ex1.fa"))
assert result == 195399
def test_fasta_iteration_long_sequences_as_file(benchmark):
result = benchmark(iterate_over_fastx_as_file,
os.path.join(BAM_DATADIR, "ex1.fa"))
assert result == 3225
def test_fastq_iteration_short_sequences(benchmark):
result = benchmark(iterate_over_fastx, os.path.join(
BAM_DATADIR, "faidx_ex1.fq"))
assert result == 3270
def test_fastq_iteration_short_sequences_without_persistence(benchmark):
result = benchmark(iterate_over_fastx, os.path.join(
BAM_DATADIR, "faidx_ex1.fq"), persist=False)
assert result == 3270
def test_fastq_iteration_short_sequences_as_file(benchmark):
result = benchmark(iterate_over_fastx_as_file,
os.path.join(BAM_DATADIR, "faidx_ex1.fq"))
assert result == 320458
|
