[Bioperl-l] Accessing /gene and /note fields in a GenBank file

Adam Witney awitney@sghms.ac.uk
Thu, 16 May 2002 15:31:25 +0100


Hi, just been trying to write a GenBank parser for a GenBank file containing
a whole genome

How do I get access to the /gene and /note fields of each gene? I have this
so far

my $gbk_obj = Bio::SeqIO->new('-file' => "gbk_file",
                              '-format' => 'GenBank');

while (my $seq = $gbk_obj->next_seq())
  {
   my @features = $seq->all_SeqFeatures;
   
   foreach my $feat (@features)
     {
      print $feat->primary_tag."\n";
      
      print $feat->start.' - '.$feat->end."\t".$feat->strand."\n";
     
      my $seq_obj = $feat->seq;

      print $seq_obj->seq."\n";
     
     }


Thanks

adam