[Bioperl-l] SearchIO speed up

Sean Davis sdavis2 at mail.nih.gov
Fri Aug 18 10:15:26 EDT 2006




On 8/18/06 9:52 AM, "Hilmar Lapp" <hlapp at gmx.net> wrote:

> 
> 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.

I can't agree more here.  There are many cases with biological data and
bioinformatics where bioperl is just not the right answer, and that is OK!

Sean



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