Bio::Seq / Steve's comments

[Georg Fuellen]

Steve wrote to Chris,
> > I'm planning to translate steve's notes into a specific list of changes to
> > make to Seq.pm and I'll post the list (along with some questions) to the
> > mailing list.
> 
> Sounds great.
Yep.
> > Making a separate Readseq.pm module seems to be fairly high up on the
> > priority list and would allow me to clean up parts of Seq.pm. I'd be
> > willing to write a simple version that uses temporary files instead of
> > bidirectional piping. The one part I would need guidance on would be the
> > interface -- I'm too new to OO/Module work to trust myself with designing
> > the most functional set of methods.
> 
> Well, I have to say that I am not terribly familiar with 'dynamic loading'
> modules either.   (Basically, we only want to call on ReadSeq if needed;
> and we want to fail cleanly if it isn't located.)   I think that looking
> at examples will be the best way forward.
Which example would you recommand ?

> I would consider coming up with a good interface for the Bio::Seq::Parse
> (see below) and Bio::SeqList (see previous mails; Georg: I'm going with
> your suggestion for name, though I still prefer Set) more crucial
> and hopefully easier than that for ReadSeq
> 
> > On a similar note, Brian Osborne bas noted that he uses the seqio package
> > for parsing because ReadSeq doesn't handle large genomic sequences (>
> > 100000 bp) that well - If we come up with a good interface for Readseq.pm
> > it would be easiy to create a seqio.pm as well.
> 
> Exactly!  Good thinking.
> 
> 
> > Would those go in Bio::Parse or Bio::Util or something? I really am quite
> > new at dealing with modules and such :)
> 
> I thought of Bio::Seq::Core or maybe Bio::Seq::Parse.  Do these seem
> reasonable?

I'd suggest Bio::Core, not Bio::Seq::Core.
Also probably Bio::Parse, not Bio::Seq::Parse. After all, ReadSeq handles
some multiple alignment formats, too.

> Bio::Seq::Util suggests end-user utilities, and therefore probably isn't a
> name we want to use.
> 
> Regards,
>  Steve

best wishes,
georg

> 
>