[Bioperl-l] Blast stuff

[Jason Stajich]

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

On Mon, 2 Dec 2002, Steve Chervitz wrote:

> --- Ewan Birney <birney@ebi.ac.uk> wrote:
> >
> > [snip]
> >
> > Bio::Tools::Blast.pm
> >
> >   I want to kill this - it has lots of confusing documentation; it is big;
> > I think Bio::SearchIO is the way forward and is stable enough to take it
> > on; I will bug fix Bio::SearchIO on spec for the 1.2 series (phew!). So...
> > can we remove it and put in a warning in a BEGIN block saying - it has
> > died, please try out Bio::SearchIO.
> >
> >
> >   SteveC and Jason - what are your votes here.
>
> R.I.P. ;-)
>
ditto.

> All of it's functionality has been taken over by other modules for some time
> now, so I feel it's ready to go away for 1.2. The Bio/Tools/Blast directory
> goes away as well.
>
> The warning message in the BEGIN block can be a bit more detailed, something
> like a table such as:
>
>   Functionality         Module to Use
>   --------------        --------------
>   BLAST parsing         Bio::SearchIO
>   BLAST running         Bio::Tools::Run::StandAloneBlast or
>                         Bio::Tools::Run::RemoteBlast
>   BLAST HTML formating  Bio::SearchIO::Writer::HTMLResultWriter
>
> TODO: Transfer the non-BLAST-specific docs from the module-level POD in
> Bio::Tools::Blast over to Bio::SearchIO, and update it for the SearchIO system.
> This would include things like how to use the SearchIO::Writer modules. This
> would be task for Jason or I.
>
> Lately I've been working on merging my psiblast.pm SearchIO module into
> Jason's blast.pm so that we can get down to just a single Blast parsing
> system.
>
woo ho!

hmmer parsing is more robustly being tested at the moment as well.

ResultTable,HitTable,HSPTable and HTML/TextResultWriter have been getting
another once over set of testing.  I expect they will get a few more
tweaks and be signed off as mature for 1.2.

> Steve
>
>
> =====
> Steve Chervitz
> sac@bioperl.org
>
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