Bioperl: Module collections...

[Steven E. Brenner]

> 
> > Looking ahead to next week when chris and I are going to 
> > get together to make the CVS system I'm downloading modules
> > to put in....
> > 
> > a) Bio::PreSeq.pm (can we start calling this Seq.pm now?)
> 
> The name change should coincide with a functionality change, namely, 
> adding a feature description mechanism. We'll have to hear from ChrisD 
> and Ian about their progress along these lines.

  I think we should think very carefully about the interfaces to
Bio::Seq.pm, and I don't know that PreSeq is tested well enough for us to
be certain that we are happy with the interfaces.    Once we create
Bio::Seq.pm, I hope that its interfaces will remain fairly constant.

  Therefore, I think it is best to keep developing PreSeq.pm for some
time.


Regarding BLAST,

   there are a fair number of modules around, and I should also note that
I believe that a new, parsable output format will be released by NCBI
before tooooo long.  We also will want to incorporate the ability to pass
more flags to control PSI-BLAST. Furthermore, I think it is helpful to
have the 'running' and the 'parsing' modules separate (with perhaps some
wrapper module which does both).  So, I think it is premature to do too
much with these modules.

Steve

=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================