[Bioperl-l] SearchIO speed up

Hilmar Lapp hlapp at gmx.net
Fri Aug 18 09:52:54 EDT 2006

On Aug 18, 2006, at 3:00 AM, Sendu Bala wrote:

> Maybe I'm wrong about that - is it reasonable to just come up with a
> whole new system for returning the results, and have users learn to  
> use
> the new system?

My take on this is that if you know your input format and you know  
how to use perl regular expressions and you need only some small  
pieces out of a report or sequence file and you just need this quick,  
then you might as well set Bioperl aside and do a straight perl one-off.

I.e., I don't think Bioperl, or any other toolkit that as its main  
benefits offers a consistent API, object model, tried-and-tested  
parsers, etc, should try to be the natural choice for a use case when  
you don't need any of these benefits.

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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