[BioRuby] Benchmarking FASTA file parsing

[Tomoaki NISHIYAMA]

Hi,

The benchmark is interesting.

> Is it possible to optimize the code without major rewriting?


Using ruby 1.9.2 (RC2) makes it 2.6 times faster without any rewriting
the bioruby parser code :)
compared to ruby-1.8 (1.8.7-p299).

$ ~/ruby192/bin/ruby benchfasta
            user     system      total        real
Hack   3.800000   0.000000   3.800000 (  3.800830)
Bio   13.090000   0.000000  13.090000 ( 13.095722)
$ ~/ruby187/bin/ruby benchfasta
            user     system      total        real
Hack   7.460000   0.000000   7.460000 (  7.456281)
Bio   34.670000   0.000000  34.670000 ( 34.680271)

As you stated 3 times faster with the hack, you may be already using  
ruby 1.9.

Anyway, I think 13 or 18 seconds for 100 M entry is fast enough and this
part will not be the bottle neck of any application.
How fast do you need it be?
-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan