Bioperl: Re:Bioperl-guts: seq/primarySeq/seqFeature

[Ewan Birney]

On Fri, 19 May 2000, James Gilbert wrote:

> 
> 
> I've fixed this in the main branch, and added
> appropriate tests, so this should now work as
> Bradley originally expected.
> 
> I don't like the fact that ->seq() on a SeqFeature
> returns a PrimarySeq object, but ->seq() on a Seq
> or PrimarySeq object returns the sequence as a
> string!

I hear you. Do you want to do the following thing ---

add a ->primary_seq method in preperation for officially
deprecating ->seq in bioperl-07 when that happens. You 
can deprecate ->seq in the main trunk now and get people to
use ->primary_seq. 

We can consider other options. Basically people can get
two types of sequence out -

	the sequence of the feature

	the entire sequence

please don't make it an argument to the method as that (perl-ish) pattern 
does not play so well in CORBA/other languages.

> 
> 	James
> 
> On Fri, 19 May 2000, Ewan Birney wrote:
> 
> > On Fri, 19 May 2000, James Gilbert wrote:
> > 
> > > 
> > > 
> > > Bradley,
> > > 
> > > OK, this explains why I've never seen this bug
> > > with the EMBL/GenBank parsing.  The feature table
> > > is parsed BEFORE the sequence, so the sequence is
> > > always empty when features are added.
> > > 
> > > I'm glad that you've got this to work with the
> > > current code base, but it ought to have worked if
> > > there was already a sequence in the Seq object.  
> > > I'll fix this in the main branch.
> > 
> > Ok guys. I am **deeply** sorry. That was clearly my bug left over from the
> > big Seq/AnnSeq/PrimarySeq rearrangement.
> > 
> > The aim is that sequence features should be attached to the primary
> > sequence of the object (*not* the Bio::Seq object) but you have to handle
> > up dates to both the PrimarySeq object of the Seq and the SeqFeature
> > Object. 
> > 
> > James - shout if you need more help. Apologies all around. I suspect
> > I will be apologising alot over the next couple of months.
> > 
> > 
> > 
> > > 
> > > 	James
> > > 
> > > On Thu, 18 May 2000, Bradley Marshall wrote:
> > > 
> > > > 
> > > > Oh wait,
> > > > 
> > > > I finally figured out how to do it.
> > > > 
> > > > The correct thing is to :
> > > > 
> > > > 1)  Create an empty Seq object.
> > > > 
> > > > 2)  Add the SeqFeatures to that EMPTY Seq.
> > > > 
> > > > 3)  Add a primary_seq to the Seq.
> > > > 
> > > > Is this correct?  Where I got into trouble before was
> > > > adding the primary_seq BEFORE I added the features.
> > > > 
> > > > Thanks
> > > > Brad
> > > > 
> > > > __________________________________________________
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> > > > 
> > > 
> > > James G.R. Gilbert
> > > The Sanger Centre
> > > Wellcome Trust Genome Campus
> > > Hinxton
> > > Cambridge                        Tel: 01223 494906
> > > CB10 1SA                         Fax: 01223 494919
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> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>. 
> > -----------------------------------------------------------------
> > 
> 
> James G.R. Gilbert
> The Sanger Centre
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge                        Tel: 01223 494906
> CB10 1SA                         Fax: 01223 494919
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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