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

[Ewan Birney]

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>. 
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