[Bioperl-l] GenBankParser comparison to bioperl parser

[Elia Stupka]

> 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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