[Bioperl-l] Blast stuff

[Steve Chervitz]

--- 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. ;-)

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. 

Steve


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

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