[BioRuby] Blast parsing speed
Yannick Wurm
Yannick.Wurm at unil.ch
Sun Sep 24 13:28:53 UTC 2006
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
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