[Bioperl-l] How to determine if GenBank record contains...

[Ryan Golhar]

That works Barry.  Thanks!

Ryan

-----Original Message-----
From: Barry Moore [mailto:bmoore at genetics.utah.edu] 
Sent: Wednesday, November 16, 2005 2:34 PM
To: golharam at umdnj.edu; bioperl-l at portal.open-bio.org
Subject: RE: [Bioperl-l] How to determine if GenBank record contains...


Ryan-

See if the two method calls in the eval statement below don't get you
what you want.

  my @CDS_feats = grep { $_->primary_tag eq 'CDS' }
$seq->get_SeqFeatures();
  print '';
  for my $feature (@CDS_feats) {
      my $location = $feature->location;
      eval {
          print "Single Sequence:\t", $location->is_single_sequence,
"\n";
          print "Split Type:\t", $location->splittype, "\n\n";
      }
  }

Barry

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l- 
> bounces at portal.open-bio.org] On Behalf Of Ryan Golhar
> Sent: Wednesday, November 16, 2005 11:38 AM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] How to determine if GenBank record contains...
> 
> How can I determine is a GenBank record containing a CDS entry has the

> join, or join-compliment keyword listed for CDS?  For example, if you 
> look up Accession AY628630 at NCBI, you'll see the CDS tag has 
> "join(...)", but DQ202315 does not.
> 
> Is there a way I can determine if a GenBank entry has this using 
> BioPerl?
> 
> Ryan
> 
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