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import gzip
import pysam
import timeit
iterations = 5
repeats = 100
print ("repeats=", repeats, "iterations=", iterations)
fn_compressed = '/tmp/windows_small.bed.gz'
fn_uncompressed = '/tmp/windows_small.bed'
def test_python_compressed():
'''iterate through with python.'''
f = gzip.open( fn_compressed)
l = len( [x.encode().split("\t") for x in f])
def test_python_uncompressed():
'''iterate through with python.'''
f = open( "windows_small.bed")
l = len( [x.split("\t") for x in f])
def test_fetch_plain():
"""Stupid test function"""
f = pysam.Tabixfile(fn_compressed)
l = len( list(f.fetch()) )
def test_fetch_parsed():
"""Stupid test function"""
f = pysam.Tabixfile(fn_compressed)
l = len( list(f.fetch( parser = pysam.asBed())) )
def test_iterator_generic_compressed():
f = gzip.open(fn_compressed)
l = len( list( pysam.tabix_generic_iterator( f, parser = pysam.asBed() )))
def test_iterator_generic_uncompressed():
f = open("windows_small.bed")
l = len( list( pysam.tabix_generic_iterator( f, parser = pysam.asBed() )))
def test_iterator_parsed_compressed():
f = gzip.open(fn_compressed)
l = len( list( pysam.tabix_iterator( f, parser = pysam.asBed() )))
def test_iterator_parsed_uncompressed():
f = open("windows_small.bed")
l = len( list( pysam.tabix_iterator( f, parser = pysam.asBed() )))
def test_iterator_file_compressed():
f = gzip.open("windows_small.bed")
l = len( list( pysam.tabix_file_iterator( f, parser = pysam.asBed() )))
def test_iterator_file_uncompressed():
f = open("windows_small.bed")
l = len( list( pysam.tabix_file_iterator( f, parser = pysam.asBed() )))
tests = ( test_python_compressed,
test_python_uncompressed,
test_fetch_plain,
test_fetch_parsed,
test_iterator_generic_compressed,
test_iterator_generic_uncompressed,
test_iterator_parsed_compressed,
test_iterator_parsed_uncompressed,
test_iterator_file_compressed,
test_iterator_file_uncompressed )
for repeat in range( repeats ):
print ("# repeat=", repeat)
for test in tests:
try:
t = timeit.timeit( test, number = iterations )
except AttributeError:
continue
print ("%5.2f\t%s" % (t,str(test)))
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