get_all_exon_sequences.pl

#!/usr/bin/env perl

use strict;
use warnings;

use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->
  load_registry_from_db(
    -host => 'mysql-eg-prod-3.ebi.ac.uk',
    -user => 'ensro',
    -port => '4243',
    -dbname => 'css_triticum_aestivum_core_30_83_1',
);

my $slice_adaptor = Bio::EnsEMBL::Registry->
  get_adaptor( 'Wheat', 'Core', 'Slice' );
warn $slice_adaptor, "\n";

my $exon_adaptor = Bio::EnsEMBL::Registry->
  get_adaptor( 'Wheat', 'Core', 'Exon' );
warn $exon_adaptor, "\n";


# get all non-redundant slices from the highest possible coordinate
# systems
my $slices = $slice_adaptor->
  fetch_all('toplevel');

for my $slice (@$slices){
    #print $slice;
    my $exons = $exon_adaptor->
      fetch_all_by_Slice($slice);
    for my $exon(@$exons){
        print ">", $exon->stable_id, "\n";
        print $exon->seq->seq, "\n";
    }
}