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"""Benchmarking module for AlignedSegment functionality"""
import timeit
iterations = 10000
repeats = 5
setup_binary_tag = """
import pysam
import array
read = pysam.AlignedSegment()
read.set_tag('FZ', array.array('H', range(1000)))
"""
setup_binary_tag_from_file = """
import pysam
with pysam.AlignmentFile("../tests/pysam_data/example_btag.bam", "rb") as inf:
read = inf.fetch().next()
"""
def test_read_binary_get_tag(read):
tags = read.get_tag('FZ')
def test_read_and_process_binary_get_tag(read):
tags = sum(read.get_tag('FZ'))
tests = (
("test_read_binary_get_tag", "setup_binary_tag"),
("test_read_binary_get_tag", "setup_binary_tag_from_file"),
("test_read_and_process_binary_get_tag", "setup_binary_tag"),
)
for repeat in range(repeats):
print ("# repeat=", repeat)
for testf, setup_name in tests:
setup = locals()[setup_name]
setup += """\nfrom __main__ import %s""" % testf
#try:
t = timeit.timeit("%s(read)" % testf, number=iterations, setup=setup)
#except AttributeError, msg:
# print msg
# continue
print ("%5.2f\t%s\t%s" % (t,testf, setup_name))
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