Perl script that uses the Ensembl Compara Perl API to print all the members of the tree containing the human ncRNA gene ENSG00000238344

exercise6_compara.pl

#!/usr/bin/env perl

# Print all the members of the tree containing the human ncRNA gene ENSG00000238344

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

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
);

my $gta = $registry->get_adaptor('multi', 'compara', 'GeneTree');
my $gma = $registry->get_adaptor('multi', 'compara', 'GeneMember');

my $gene_member = $gma->fetch_by_source_stable_id("ENSEMBLGENE", "ENSG00000238344"); # Get the 'GeneMember' object for the gene ENSG00000238344
my $genetree = $gta->fetch_default_for_Member($gene_member); 

my @mem = @{$genetree->get_all_Members()};
foreach my $mem (@mem) {
   my $stable_id = $mem->stable_id();
   print "___ $stable_id\n"; 
}