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

[James Gilbert]

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!

	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
> > > 
> > > __________________________________________________
> > > Do You Yahoo!?
> > > Send instant messages & get email alerts with Yahoo! Messenger.
> > > http://im.yahoo.com/
> > > =========== Bioperl Project Mailing List Message Footer =======
> > > Project URL: http://bio.perl.org
> > > For info about how to (un)subscribe, where messages are archived, etc:
> > > http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl-guts.html
> > > ====================================================================
> > > 
> > 
> > James G.R. Gilbert
> > The Sanger Centre
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge                        Tel: 01223 494906
> > CB10 1SA                         Fax: 01223 494919
> > 
> > =========== Bioperl Project Mailing List Message Footer =======
> > Project URL: http://bio.perl.org/
> > For info about how to (un)subscribe, where messages are archived, etc:
> > http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
> > ====================================================================
> > 
> 
> -----------------------------------------------------------------
> 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

=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================