[Bioperl-l] Re: [Bioperl-announce-l] bioperl 1.2.3 RC1

[Jason Stajich]

On Wed, 17 Sep 2003, Steve Chervitz wrote:

> On Monday, Sep 15, 2003, at 10:05 US/Pacific, Jason Stajich wrote:
> >
> > Developers:
> >  If you have any last minute changes - you need to get them in by
> > tomorrow
> >  or let me know what you still have pending and I can hold up making a
> >  final release.
>
> I put in a small addition to SeqIO::fasta that allows you to specify
> which type of identifier to appear after the '>' in the generated fasta
> output (e.g., accession, accession.version, display, or primary). The
> new method is called preferred_id_type. This is only applicable to
> fasta format; other formats have special slots for different types of
> identifiers, so it didn't make sense to put this in SeqIO.pm. I also
> added a test for it in SeqIO.t.
>
> Jason: Since this was such a trivial addition and doesn't affect
> existing functionality, I put in on the 1.2 branch as well as
> bioperl-live. However, since it is new functionality, I should have put
> it on the main trunk only. Let me know if you want to back it out of
> the branch.

It is fine Steve - a couple of new features have already sneaked their way
onto the branch.  I think it will be a many months until 1.4 is ready to
go stable so I'd rather put some of the (simple) new features out there if
they don't cause any backwards compatability problems.

>
> One issue I haven't addressed is how to deal with SeqIO::MultiFile.
> This module should delegate any method calls it can't handle (such as
> preferred_id_type) to its current SeqIO object. This would also address
> other format-specific methods such as SeqIO::fasta::width().
>
> Steve
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu