[Bioperl-l] GenBankParser comparison to bioperl parser

[Ian Korf]

I'll de-lurk for this.

I, for one, think that a bio-util-perl project would be a good 
idea. Not everyone wants or needs the whole of bioperl. 
Sometimes, a small utility outside the framework is useful. 
Analogously, I use a full-featured text editor that counts 
letters, words, paragraphs etc, but I still find myself using wc 
from time to time.

I think that if something is going to be part of bioperl, it 
ought to have the same consistent interface. But I like what 
John has done, both at the interface and implementation level. 
Is it possible to leave John's parser the way it is and offer a 
bioperl interface to it?

-Ian

On Thursday, September 12, 2002, at 09:08 AM, Elia Stupka wrote:

>> As Jason says we are both aware of the performance problems in 
>> the bioperl
>> parsers, and have some suspicision of where they are. In fact, 
>> I am not
>> 100% sure if my speed fixes went into the main trunk or the branch.
>
> Hello guys, I've been following this discussion and I am not 
> sure what the
> conclusion is, but it looks to me like you are saying "yes your 
> parser is
> faster but we know why ours is slow so when we can we will try 
> to get your
> speeds", without taking the code in as part of bioperl.
>
> Doesn't that go against "who codes it wins it"? I mean if somebody is
> interested in a non-bio-object-centric way of parsing that is 
> much faster,
> doesn't it make sense to take it in as a worthy contribution to 
> bioperl?
>
> What it seems to suggest in the long run is the setting up of a 
> separate
> bio-util-perl project where useful but not wonderfully integrated stuff
> gets developed, and surely that's not what we want to see happening?
>
> Basically I am suggesting that the parser should be commited in
> bioperl. This will make it easier for all of us to assess it 
> and also to
> reuse concepts to improve our own parsers, and then once our 
> parsers are
> so good and if nobody shouts they love the other one, we can 
> always remove
> it.
>
> My two stirrin-the-waters cents,
>
> Elia
>
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