get_cds

#!/usr/bin/perl

use strict;
use Bio::SeqIO;
use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
    );

open(SPECIES, "<species_list.txt");
my @species = <SPECIES>;

my $n = $ARGV[0];
my $s = $species[$n];
chomp $s;

open(OUTFILE, '>' . $s . '_cds.fa');
my $gene_adaptor =
    Bio::EnsEMBL::Registry->get_adaptor( $s, 'Core',
                                         'Gene' );

my @genes = @{ $gene_adaptor->fetch_all_by_biotype('protein_coding') };

foreach my $gene (@genes) {
    my @transcripts = ( $gene->canonical_transcript() );
    # my @transcripts = @{$gene->get_all_Transcripts()};

    foreach my $transcript (@transcripts) {
        print OUTFILE ">", $transcript->stable_id, "\n", $transcript->translateable_seq, "\n";
    }
}

close(OUTFILE);