[BioRuby] Blast parsing speed

[Yannick Wurm]

Hi,
I have been happily using bioruby for the past year or so for my post- 
blast analyses. Occasionally, I will have ~ 1gb blast result files  
that need to be parsed. Here my machine may start paging and slows to  
a crawl.

Thus I wonder:
	- has anyone benchmarked bioruby, bioperl, biojava, biopython when  
processing the same file to compare speed and memory usage?
	- For the sake of future compatibility, I have been use blast's xml  
output. How much slower is it is to parse such an xml file relative  
to a "normal" or tabular blast output?

Cheers,

Yannick

--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html