[Bioperl-l] GCG MSF format alignments

[Ewan Birney]

On Fri, 9 Mar 2001, Hilmar Lapp wrote:

> Peter Schattner wrote:
> > 
> > > Regarding the ~ characters ... my primitive understanding suggests this
> > > throws an exception in Bio::Primaryseq::seq with a message that '[some
> > > sequence ~~~] does not look healthy'.
> > 
> > I've had this problem too in other contexts.  Bio::Primaryseq is
> > currently rather strict about what it allows in asequence.  I would
> > prefer to see it issue a warning rather than die when it comes across a
> > bad character (what do you think about that Ewan? Hilmar? Jason?)
> 
> I actually like the exception being thrown there, even though I bumped
> into this several times, too. However, it always indicated a bug.
> 
> I'd actually prefer this being solved by creating a specialized class
> that specifically allows for additional characters as they are used in
> e.g. alignments. This should go under Bio::Seq::<AlignedSeq>.pm
> (replace <...> with whatever you like better). Ideally Bio::PrimarySeq
> (or maybe better Bio::PrimarySeqI?) has a method boolean
> validate_seq(), and depending on its return value seq() throws an
> exception. So, in your deriving implementation you'd only have to
> override validate_seq(). (As a matter of fact, there is no
> validate_seq() right now :|
> 
> Does this make sense to anyone?

Yup. The refinement here is that Alignments use LocatableSeq so that's the
place to put it (perhaps LocatableSeq should migrate to AlignedSeq...)


> 
> 	Hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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