[Bioperl-l] GenBankParser comparison to bioperl parser

[Ewan Birney]

On Thu, 12 Sep 2002, 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,


Sure - set up a new repository - help John commit it, lets do it.


I'm not going to do it ;)


> 
> Elia
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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