[Bioperl-l] How to retrieve introns / exons from EMBL?

[Jason Stajich]

What accession number are you trying for, so we can test it too...

On Fri, 13 Jun 2003 ole.st at gmx.de wrote:

> Brian,
>
> I just read the point Q5.2 in the FAQ about retrieving all the features from
> a
> sequence. (was this the question you mentioned ?)  I used the sample code
> to browse some entries of EMBL, but it doesn't work: I don't get any
> features
> with a primary tag like "exon" as described in the FAQ.  My perl program
> looks like
> this:
>
> $EMBL = new Bio::DB::EMBL->new();
> $seq = $EMBL->get_Seq_by_id($id);
> @genes = grep {$_->primary_tag eq 'exon' } $seq->all_SeqFeatures();
>
> foreach $exon ( @genes) {
> print "Exon!\n";
> }
>
> I've got no idea why it doesn't work.
>
> Ole
>
> > Ole,
> >
> > There is a question and answer in the FAQ about this, but I don't know if
> > it's sufficient. Why don't you take a look and tell us if you need
> > additional information. Certainly not a stupid question.
> >
> > Brian O.
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at portal.open-bio.org
> > [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Ole
> > Schulz-Trieglaff
> > Sent: Friday, June 13, 2003 11:05 AM
> > To: bioperl-l at portal.open-bio.org
> > Subject: [Bioperl-l] How to retrieve introns / exons from EMBL?
> >
> > Hello,
> >
> > I'm a bioperl beginner and I apologize if this is a rather stupid
> > question. But I'm looking for an easy method to extract the introns/exons
> > of an EMBL-Entry with the start and stop position. I read the
> > documentation of the Seq/LiveSeq classes but it is rather short and
> > difficult to understand.
> >
> >
> > Thank you very much,
> >
> > Ole Schulz-Trieglaff
> >
> > Berlin, Germany
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>

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