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

ole.st at gmx.de ole.st at gmx.de
Fri Jun 13 20:29:47 EDT 2003


I just read the point Q5.2 in the FAQ about retrieving all the features from
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
with a primary tag like "exon" as described in the FAQ.  My perl program
looks like

$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,
> 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
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> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

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