Added new 'species' argument to load_registry_from_db():

Arg [SPECIES]:  (optional) string
                By default, all databases that are found on the server
                and that corresponds to the correct release are probed
                for aliases etc.  For some people, depending on where
                they are in the world, this might be a slow operation.
                With the '-species' argument, one may reduce the startup
                time by restricting the set of databases that are probed
                to those of a particular species.

                Note that the latin name of the species is required,
                e.g., 'homo sapiens', 'gallus gallus', 'callithrix
                jacchus' etc.  It may be the whole species name, or only
                the first part of the name, e.g. 'homo', 'gallus', or
                'callithrix'.  This will be used in matching against the
                name of the databases.

modules/Bio/EnsEMBL/Registry.pm

@@ -1317,13 +1317,31 @@ sub load_registry_from_url {
   Arg [VERBOSE]: (optional) boolean
                 Whether to print database messages.
 
+  Arg [SPECIES]: (optional) string
+                By default, all databases that are found on the
+                server and that corresponds to the correct release
+                are probed for aliases etc.  For some people,
+                depending on where they are in the world, this might
+                be a slow operation.  With the '-species' argument,
+                one may reduce the startup time by restricting the
+                set of databases that are probed to those of a
+                particular species.
+
+                Note that the latin name of the species is required,
+                e.g., 'homo sapiens', 'gallus gallus', 'callithrix
+                jacchus' etc.  It may be the whole species name,
+                or only the first part of the name, e.g. 'homo',
+                'gallus', or 'callithrix'.  This will be used in
+                matching against the name of the databases.
+
   Arg [DB_VERSION]: (optional) integer
-                By default, only databases corresponding to this API
-                version are loaded. This allows the script to use
-                databases from another version although it might not
-                work properly.  This option should only be used for
-                production or testing purposes and if you really
-                know what you are doing.
+                By default, only databases corresponding to the
+                current API version are loaded.  This argument
+                allows the script to use databases from another
+                version although it might not work properly.  This
+                argument should only be used for production or
+                testing purposes and if you really know what you are
+                doing.
 
   Arg [WAIT_TIMEOUT]: (optional) integer
                 Time in seconds for the wait timeout to happen.
@@ -1333,7 +1351,7 @@ sub load_registry_from_url {
                 getting deleted.  Only set this if you are having
                 problems and know what you are doing.
 
-   Arg [-NO_CACHE]: (optional) int 1
+   Arg [-NO_CACHE]: (optional) boolean
                 This option will turn off caching for slice
                 features, so, every time a set of features is
                 retrieved, they will come from the database instead
@@ -1351,7 +1369,7 @@ sub load_registry_from_url {
       -verbose => '1'
     );
 
-  Description: Will load the correct versions of the ensembl
+  Description: Will load the correct versions of the Ensembl
                databases for the software release it can find on a
                database instance into the registry.  Also adds a set
                of standard aliases.
@@ -1364,14 +1382,20 @@ sub load_registry_from_url {
 sub load_registry_from_db {
   my ( $self, @args ) = @_;
 
-  my ( $host, $port, $user, $pass, $verbose, $db_version, $wait_timeout,
-    $no_cache )
-    = rearrange( [
-      'HOST',    'PORT',       'USER',         'PASS',
-      'VERBOSE', 'DB_VERSION', 'WAIT_TIMEOUT', 'NO_CACHE'
-    ],
-    @args
-    );
+  my ( $host,         $port,     $user,
+       $pass,         $verbose,  $db_version,
+       $wait_timeout, $no_cache, $species )
+    = rearrange( [ 'HOST',         'PORT',
+                   'USER',         'PASS',
+                   'VERBOSE',      'DB_VERSION',
+                   'WAIT_TIMEOUT', 'NO_CACHE',
+                   'SPECIES' ],
+                 @args );
+
+  if ( defined($species) ) {
+    $species = lc($species);
+    $species =~ tr/ -/__/;
+  }
 
   my $go_version       = 0;
   my $ontology_version = 0;
@@ -1431,9 +1455,16 @@ sub load_registry_from_db {
       }
     } elsif ( $db =~ /^([a-z]+_[a-z0-9]+_[a-z]+(?:_\d+)?)_(\d+)_(\w+)/ )
     {
-      if ( $2 eq $software_version ) {
-        $temp{$1} = $2 . "_" . $3;
+      # Species specific databases (core, cdna, vega etc.)
+
+      my ( $one, $two, $three ) = ( $1, $2, $3 );
+
+      if ( !defined($species) || $one =~ /^$species/ ) {
+        if ( $two eq $software_version ) {
+          $temp{$one} = $two . "_" . $three;
+        }
       }
+
     } else {
       # warn( sprintf( "Skipping database '%s'\n", $db ) );
     }