Perl script that uses the Ensembl Compara Perl API to count the number of “one2one” orthologues between human and mouse

exercise8_compara.pl

#!/usr/bin/env perl

# Count the number of “one2one” orthologues between human and mouse
# Note: this script gives a warning about some variable declaration within the Compara API.

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

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

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

# A 'MethodLinkSpeciesSet' adaptor can be used to get orthologs between a pair of species. 
my $mlss_adaptor = $registry->get_adaptor('Multi', 'compara', 'MethodLinkSpeciesSet');
my $this_mlss = $mlss_adaptor->fetch_by_method_link_type_registry_aliases('ENSEMBL_ORTHOLOGUES', ['human', 'mouse']);

# Now get all the homology relationships for this 'MethodLinkSpeciesSet' object:
my $ha = $registry->get_adaptor('multi', 'compara', 'Homology');
my @homologies = @{ $ha->fetch_all_by_MethodLinkSpeciesSet($this_mlss, -ORTHOLOGY_TYPE => 'ortholog_one2one')};

my $num_one2one = 0;
foreach my $homology (@homologies){
  my $desc = $homology->description();
  if ($desc ne 'ortholog_one2one') { print STDERR "ERROR: desc $desc\n"; exit;}
  $num_one2one++;
}
# Alternatively you could just do:
# $num_one2one = scalar(@homologies);
print "Total number of human-mouse one-2-one orthologs: $num_one2one\n";
# get 15678