Method much slower than function?

idoerg at gmail.com idoerg at gmail.com
Thu Jun 14 02:40:12 CEST 2007


Hi all,

I am running Python 2.5 on Feisty Ubuntu. I came across some code that
is substantially slower when in a method than in a function.

################# START SOURCE #############
# The function

def readgenome(filehandle):
	s = ''
	for line in filehandle.xreadlines():
		if '>' in line:
			continue
		s += line.strip()
	return s

# The method in a class
class bar:
	def readgenome(self, filehandle):
		self.s = ''
		for line in filehandle.xreadlines():
			if '>' in line:
				continue
			self.s += line.strip()

################# END SOURCE ##############
When running the function and the method on a 20,000 line text file, I
get the following:

>>> cProfile.run("bar.readgenome(open('cb_foo'))")
         20004 function calls in 10.214 CPU seconds

   Ordered by: standard name

   ncalls  tottime  percall  cumtime  percall
filename:lineno(function)
        1    0.000    0.000   10.214   10.214 <string>:1(<module>)
        1   10.205   10.205   10.214   10.214 reader.py:11(readgenome)
        1    0.000    0.000    0.000    0.000 {method 'disable' of
'_lsprof.Profiler' objects}
    19999    0.009    0.000    0.009    0.000 {method 'strip' of 'str'
objects}
        1    0.000    0.000    0.000    0.000 {method 'xreadlines' of
'file' objects}
        1    0.000    0.000    0.000    0.000 {open}


>>> cProfile.run("z=r.readgenome(open('cb_foo'))")
         20004 function calls in 0.041 CPU seconds

   Ordered by: standard name

   ncalls  tottime  percall  cumtime  percall
filename:lineno(function)
        1    0.000    0.000    0.041    0.041 <string>:1(<module>)
        1    0.035    0.035    0.041    0.041 reader.py:2(readgenome)
        1    0.000    0.000    0.000    0.000 {method 'disable' of
'_lsprof.Profiler' objects}
    19999    0.007    0.000    0.007    0.000 {method 'strip' of 'str'
objects}
        1    0.000    0.000    0.000    0.000 {method 'xreadlines' of
'file' objects}
        1    0.000    0.000    0.000    0.000 {open}


The method takes > 10 seconds, the function call 0.041 seconds!

Yes, I know that I wrote the underlying code rather inefficiently, and
I can streamline it with a single file.read()  call instead if an
xreadlines() + strip loop. Still, the differences in performance are
rather staggering! Any comments?

Thanks,

Iddo




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