[Bioperl-l] 0.7 release: Blast

Ewan Birney birney@ebi.ac.uk
Tue, 14 Nov 2000 17:35:02 +0000 (GMT)

On Tue, 14 Nov 2000, Hilmar Lapp wrote:

> Ewan Birney wrote:
> > code. However, I don't think we will be able to tease out the Root::Object
> > >from the blast code, and we can't remove the code (backward compatibility)
> > even though we have BPLite in.
> > 
> Just to mention, the Blast module offers also more functionality than
> BPlite (which is probably intentional, as the name BPlite implies). I'm
> for instance using the frac_identical() (_conserved etc) methods
> exploiting the tiling of HSPs, which is what you need if you want to
> know how much of your query sequence is matched by the subject (and vice
> versa).

Agreed. I'm sorry - I often sound overly negative about BLAST - it does a
great deal and is very useful. I just find it scary down there...

> So, I personally don't want to let people get the impression that in
> fact we want to abandon Blast.pm sooner or later. Maintenance of that
> module is, however, obviously a problem, as SteveC seems to be too busy
> with other things, and it is too complicated for someone else of the
> developers to jump in.

I agree on this as well.

> The question is whether as a consequence Blast.pm will have to be
> abandoned at some time though (contradicting myself :) In this case I
> think it is essential to migrate some of the important functionality of
> Blast.pm that makes its difference to Ian Korf's code. Again, this is
> not so simple in a 'logistic' sense, because BPlite in BioPerl is only a
> ported version (how much does it differ from the original version?
> Lorenz?)

We are caught in between a rock and a hard place.

	- blast modules are difficult to maintain 

	- bplite was designed to be lite not heavy and ian doesn't want to
maintain this inside bioperl as he (rightly) thinks that this means that
bplite will become bpheavy

What do we do -

	- battle on with blast modules?

	- fork bplite?

	- rewrite?

> When I noticed that this is sort of off topic, I changed the subject
> line; it's probably not even something we can or should address for the
> 0.7 release.

Definitely not ;)

> What do people think?
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420