Adding a registry version to CliHelper

modules/Bio/EnsEMBL/Utils/CliHelper.pm

@@ -82,6 +82,7 @@ use Carp;
 use Data::Dumper;
 use Getopt::Long qw(:config auto_version no_ignore_case);
 
+use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::DBSQL::DBConnection;
 use Bio::EnsEMBL::DBSQL::DBAdaptor;
 
@@ -251,4 +252,35 @@ sub get_dbas_for_opts {
 	}
 	return $dbas;
 }
+
+=head2 load_registry_for_opts
+
+  Arg [1]    	: Hash of options (e.g. parsed from command line options by process_args()) 
+  Arg [2]     : Optional prefix to use when parsing e.g. dna or master 
+  Description	: Loads a Registry from the given options hash. If a C<registry> 
+                option is given then the code will call C<load_all>. Otherwise
+                we use the database parameters given to call 
+                C<load_registry_from_db()>.
+  Returntype  : Integer of the number of DBAdaptors loaded
+  Status      : Under development
+
+=cut
+
+sub load_registry_for_opts {
+  my ($self, $opts, $prefix) = @_;
+  $prefix ||= q{};
+  if($opts->{registry}) {
+    my $location = $opts->{registry};
+    return Bio::EnsEMBL::Registry->load_all($location);
+  }
+  my ( $host, $port, $user, $pass ) = map { $prefix . $_ } qw(host port user pass);
+  my %args = (
+    -HOST => $opts->{$host},
+    -PORT => $opts->{$port},
+    -USER => $opts->{$user},
+  );
+  $args{-PASS} = $opts->{$pass};
+  return Bio::EnsEMBL::Registry->load_registry_from_db(%args);
+}
+
 1;