An Ensembl script for finding all the available introns for a single Gene for each of its transcripts & printing them to screen

dicty_introns.pl

=head1 LICENSE

 Copyright (c) 1999-2011 The European Bioinformatics Institute and
 Genome Research Limited.  All rights reserved.

 This software is distributed under a modified Apache license.
 For license details, please see

   http://www.ensembl.org/info/about/code_licence.html

=cut

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(
  -HOST => 'mysql.ebi.ac.uk',
  -PORT => 4157,
  -USER => 'anonymous'
);

my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor('Dictyostelium discoideum', 'core');
my $gene_adaptor = $dba->get_GeneAdaptor();
my $stable_id = 'DDB_G0280943';

my $gene = $gene_adaptor->fetch_by_stable_id($stable_id);
foreach my $transcript (@{$gene->get_all_Transcripts()}) {
  print $transcript->stable_id(), "\n";
  foreach my $intron (@{$transcript->get_all_Introns}) {
    print $intron->seq_region_start.' - '.$intron->seq_region_end, "\n";
  }
}