[Bioperl-l] Annotation & Feature HOWTO

[Marc Logghe]

I think it is better to first check whether the feature has the tag or not and then start the loop:
use Bio::SeqIO;

my $seqio_object = Bio::SeqIO->new( -file => $gb_file );
my $seq_object   = $seqio_object->next_seq;

foreach my $feat_object ( $seq_object->get_SeqFeatures )
{
  if ( $feat_object->primary_tag eq "CDS" )
  {
    print $feat_object->spliced_seq->seq, "\n";

    # e.g. 'ATTATTTTCGCTCGCTTCTCGCGCTTTTTGAGATAAGGTCGCGT...'
    if ( $feat->has_tag('gene') )
    {
      foreach my $val ( $feat->get_tag_values('gene') )
      {
        print "gene: ", $val, "\n";

        # e.g. 'NDP', from a line like '/gene="NDP"'
      }
    }
  }
}


> -----Original Message-----
> From: James Wasmuth [mailto:james.wasmuth at ed.ac.uk]
> Sent: dinsdag 18 mei 2004 10:55
> To: brian_osborne at cognia.com; bioperl-l at bioperl.org
> Subject: [Bioperl-l] Annotation & Feature HOWTO
> 
> 
> Hi Brian,
> 
> about a third of the way down the page of the Annotation & Feature 
> HOWTO  is the line.
> 
> foreach my $val ($feat->get_tag_values('gene')
> if ($feat->has_tag('gene')) {
> 
> 
> The parentheses don't add up, and no matter where I put new 
> ones I get a 
> syntax error
> 
> near ")
>                             if"
> 
> Can someone lift the fog covering my eyes?
Problem was here that the curly was missing:
foreach my $val ($feat->get_tag_values('gene') { # <==============
if ($feat->has_tag('gene')) {

HTH,
Marc