Simple code example to retrieve annotati …

Simple code example to retrieve annotations

 1 #!/usr/bin/perl -w
  2     
  3 use strict;
  4 use Carp;
  5 use Bio::SeqIO;
  6 
  7 my $embl_file = shift;
  8 my $informat = "embl";
  9 
 10 my $seq_in = Bio::SeqIO -> new(-file => "<$embl_file",
 11                                -format => $informat)
 12                 or croak("File Open Error: $embl_file\n");
 13 
 14 while (my $seq = $seq_in->next_seq) {
 15 
 16 
 17 # ID
 18 $seq->primary_seq->display_id();
 19 # AC
 20 $seq->primary_seq->accession_number();
 21 
 22 # DE
 23 $seq->primary_seq->desc();
 24 
 25 # CC
 26 my $annotation = $seq->annotation();
 27 my @comments = $annotation->get_Annotations('comment');
 28 foreach my $comment (@comments){
 29     print $comment->as_text;
 30 }
 31 
 32 
 33     print "\n";
 34 }
 35 
 36 $seq_in->close() or croak("Close error: $embl_file\n");