[Open-bio-l] Re: [Bioperl-guts-l] bioperl commit

[Steve Chervitz]

Brian,

Looks like the searchio/writer directory didn't make it back into scripts. Did
you intend to leave these out? They're useful for showing how to work with the
new SearchIO::Writer system, and will also be of use as Jason and I work on
migrating functionality from the psiblast.pm to blast.pm SearchIO modules. Can
you add them in again?

Also, the various blast output samples from examples/blast/out never got added
back. Maybe this is an opportunity to do something novel... Wouldn't it be
great  if all of the Bio* teams could share the same set of sample Blast (and
other program) output files? This way, all the Bio* camps can profit from
having a common, comprehensive set of sample files. This would help reduce
duplicated effort across projects and may even foster some healthy competition
(e.g., "the bioxxx blast parser can handle more sample files than the bioyyy
blast parser").  

Actually, I've always envied Jeff's suite of Blast output files over in
biopython/Tests/Blast but thought it would be silly to just copy them over into
the bioperl cvs. The biojava folks have their own samples and I'd imagine the
bioruby folks have been amassing their own collection as well.

What do people think about creating a new cvs module called "biodata" where we
can start housing these things? Each Bio* release could include the latest
export from biodata. This is one area that is truly cross-platform and
cross-language.

Steve

--- Brian Osborne <bosborne@bioperl.org> wrote:
> 
> bosborne
> bioperl-live/examples/searchio/writer custom_writer.pl hitwriter.pl
> hitwriter2.pl hitwriter3.pl hspwriter.pl rawwriter.pl resultwriter.pl
> Mon Aug 26 07:45:19 EST 2002
> Update of /home/repository/bioperl/bioperl-live/examples/searchio/writer
> In directory pw600a.bioperl.org:/tmp/cvs-serv19317/examples/searchio/writer
> 
> Removed Files:
> 	custom_writer.pl hitwriter.pl hitwriter2.pl hitwriter3.pl 
> 	hspwriter.pl rawwriter.pl resultwriter.pl 
> Log Message:
> Merging scripts and examples...
> 
> _______________________________________________
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=====
Steve Chervitz
sac@bioperl.org

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