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
|
"""Benchmarking module for AlignmentFile functionality"""
import os
import subprocess
import pysam
from TestUtils import BAM_DATADIR
def count_number_lines_with_samtools(fn):
os.system("samtools view {} | wc -l > /dev/null".format(fn))
return 3270
def count_number_lines_with_samtoolspipe(fn):
with subprocess.Popen(["samtools", "view", fn],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE) as proc:
return len(proc.stdout.readlines())
def count_number_lines_with_pysam(*args, **kwargs):
with pysam.AlignmentFile(*args, **kwargs) as inf:
return len(list(inf.fetch()))
def test_count_number_lines_from_sam_with_samtools(benchmark):
result = benchmark(count_number_lines_with_samtools,
os.path.join(BAM_DATADIR, "ex2.sam"))
assert result == 3270
def test_count_number_lines_from_sam_with_samtoolspipe(benchmark):
result = benchmark(count_number_lines_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.sam"))
assert result == 3270
def test_count_number_lines_from_sam_with_pysam(benchmark):
result = benchmark(count_number_lines_with_pysam,
os.path.join(BAM_DATADIR, "ex2.sam"), "r")
assert result == 3270
def test_count_number_lines_from_bam_with_samtools(benchmark):
result = benchmark(count_number_lines_with_samtools,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 3270
def test_count_number_lines_from_bam_with_samtoolspipe(benchmark):
result = benchmark(count_number_lines_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 3270
def test_count_number_lines_from_bam_with_pysam(benchmark):
result = benchmark(count_number_lines_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 3270
|
