Re: (Golf) RNA Genetic Code Translator

So I got around to benchmarking today. I was struck by the large variability in the benchmarks--2 orders of magnitude difference. So can someone explain why tadman's and MeowChow's subs are so much faster?

tadman original: timethis 100000: 70 wallclock secs (70.00 usr + 0.02 sys = 70.02 CPU) @ 1428.16/s (n=100000)

MeowChow: timethis 100000: 13 wallclock secs (12.25 usr + 0.00 sys = 12.25 CPU) @ 8163.27/s (n=100000)

no_slogan: timethis 100000: 81 wallclock secs (78.22 usr + 0.04 sys = 78.26 CPU) @ 1277.79/s (n=100000)

srawls: timethis 100000: 56 wallclock secs (53.80 usr + 0.07 sys = 53.87 CPU) @ 1856.32/s (n=100000)

tachyon: timethis 100000: 90 wallclock secs (89.07 usr + 0.06 sys = 89.13 CPU) @ 1121.96/s (n=100000)

tadman golf: timethis 100000: 1 wallclock secs ( 0.83 usr + 0.00 sys = 0.83 CPU) @ 120481.93/s (n=100000)

Scott

Experimental method:

I placed each sub in a holder script and executed it. The script looked like this:

#!/usr/bin/perl

use Benchmark;
my $iter=100000;

while (<DATA>){ #tadman original

 timethis($iter, sub {

$_=pop;y/UCAG/0123/;s/(.)(.)(.)/substr
"FFLLSSSSYY..CC.WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
,$1<<4|$2<<2|$3,1/ge;y/0123//d;$_

  });


}

__DATA__
yada yada... the CFTR mRNA from above.
[download]

Comment on Re: (Golf) RNA Genetic Code Translator Download Code

Replies are listed 'Best First'.
Re^2: (Golf) RNA Genetic Code Translator by tadman (Prior) on Jul 09, 2001 at 22:13 UTC
I think MeowChow's would be nearly as fast, except that for reasons of brevity it performs this crazy map operation on every base-pair triplet substitution. On this train of thought, is there such as thing as a Benchmark-type routine that will test performance on a variety of data sizes? So many times people benchmark a variety of routines with only one set of data, which has the result of being a 1-dimensional test where there are actually 2 independent variables (function and data set size). In line with Big-O Notation, is it possible and/or has someone written a Benchmark-type module which would estimate what kind of O(f(n)) function would best represent how the algorithm in question scales? Certainly not trivial by any means, but not impossible either.	[reply]
Re: Re^2: (Golf) RNA Genetic Code Translator by scain (Curate) on Jul 09, 2001 at 22:29 UTC
This is not exactly what you asked for, but it would be easy to place several sequences in the `__DATA__` chunk, one to a line, and since the `timethis` is in a `while` loop, it will iterate over each seqence. If you wanted to be really anal, you could then pipe the output to another perl program to parse and do statistics. Scott	[reply] [d/l] [select]


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