[Bioperl-l] Blast stuff

[Ewan Birney]

On Tue, 3 Dec 2002, Steve Chervitz wrote:

> Ewan,
> 
> The merging does in fact refer to adding psiblast parsing functionality to
> blast.pm so that psiblast.pm can be obsoleted and we can simplify the SearchIO
> code base. Yes, this is a destabilizing change in the short-term, but
> stabilizing in the long-term.
> 
> Jason and I have been talking about targeting this for 1.2, but I'm having
> doubts because it is a fairly major undertaking, and there's time pressure to
> release 1.2. So I think we'd all be more comfortable if it was done first in a
> developer's release to allow for more testing.
> 

Yes - I agree. I think this has to happen in the 1.3 to 1.4 series.


> As for work on the objects produced by the parsers, I've already committed code
> that allows the generic search objects work with the writers (specifically to
> allow GenericHits to undergo HSP tiling).
> 
> Perhaps the best strategy for 1.2 is to focus on testing the GenericHit HSP
> tiling and beefing up the SearchIO docs. The psiblast.pm -> blast.pm merging
> would then be deferred until after 1.2. Sound good? (BTW, what's the target
> date for 1.2?)


This sounds ideal. 1.2 release date is targetted at 31st Dec 2002 ;) (one 
day before NCBI supposedly switch off their older web tools). I want to 
realistically have at the very least, very solid release candidates if not 
the whole thing by mid Dec. Does not seem impossible to do.


> 
> Steve
> 
> --- Ewan Birney <birney@ebi.ac.uk> wrote:
> > 
> > Steve - what does merging psiblast and blast parsing in the searchIO mean?
> > I don't want any destabilising moves on the code base as we head towards
> > 1.2 (i know you too well steve....)
> > 
> > 
> > So...
> > 
> >   Making psiblast.pm produce the same objects as blast.pm and so can be
> > used by the same set of results writers - GOOD
> > 
> >   Killing psiblast.pm and merging into blast.pm - BAD - destablising.
> > 
> > 
> > 
> > make sure you don't leave it to the last minute to put changes in.
> > remember the matrix of platforms-and-perl-versions is huge for testing.
> > 
> > 
> > 
> > 
> 
> 
> 
> =====
> Steve Chervitz
> sac@bioperl.org
> 
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