[Bioperl-l] SearchIO speed up

Chris Fields cjfields at uiuc.edu
Mon Aug 14 11:30:34 EDT 2006


>> ...I hesitate to try to "clarify", but this is as much for my own  
>> good as for
>> that of others.  I think the distinction here is between "random  
>> access",
>> which is probably not necessary for Blast parsing
>
> Not 'necessary', but if you don't make use of random access you lose a
> lot of the possible advantages of having a pull-parser (ie. will be
> forced to parse and store more data than the user strictly needs).
>
> It'll become clearer when I make some code available, can continue
> discussion then.

'Don't stand in the way of someone who threatens to code!'  Where  
have I heard that before??

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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