Bioperl: Module collections...
Steven E. Brenner
Sat, 1 Aug 1998 16:03:31 +0100
> > 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
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.
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