diff --git a/misc-scripts/add_species_aliases.pl b/misc-scripts/add_species_aliases.pl
deleted file mode 100755
index fe2694011f87ab4469b27d90b93b655a2157c778..0000000000000000000000000000000000000000
--- a/misc-scripts/add_species_aliases.pl
+++ /dev/null
@@ -1,221 +0,0 @@
-#!/usr/bin/env perl
-
-use strict;
-use warnings;
-
-use Bio::EnsEMBL::Registry;
-
-use Getopt::Long qw( :config no_ignore_case );
-
-#-----------------------------------------------------------------------
-
-sub usage {
- print("Info:\n");
- print <<EOT;
- Script to populate the meta table with species aliases.
-
- >> The Release Coordinator runs this script <<
- >> when all databases have been copied over <<
- >> to the staging severs. <<
-
- The script reads the already existing aliases from the
- meta table (meta_key 'species.alias') and adds to this
- aliases computed from the species name. It also uses the
- information stored for the meta_keys species.taxonomy_id,
- species.common_name, species.ensembl_common_name, and
- species.ensembl_alias_name as aliases.
-
- If the -n or --dryrun options are *not* specified, the existing
- list of aliases is appended with any missing aliases. In any
- case, the list of aliases will be displayed on the console.
-
- The database will not be written to if there are no new aliases
- to be written to the meta table.
-
- If the -d or --dbname options are *not* used, the script will
- iterate over all Core databases. If the -d or --dbname option
- *is* used, only that Core database will be examined.
-
- This script assumes that the database is a single-species
- database.
-
- This script does not check for alias duplications between
- species.
-
-
-EOT
-
- print("Usage:\n");
- printf( "\t%s\t[-n] -h dbhost [-P dbport] \\\n"
- . "\t%s\t-u dbuser [-p dbpass] \\\n"
- . "\t%2\$s\t[-d dbname]\n",
- $0, ' ' x length($0) );
- print("\n");
- printf( "\t%s\t-?\n", $0 );
- print("\n");
- print("Arguments:\n");
- print("\t-n/--dryrun\t\tDry run, don't write to database\n");
- print("\t-h/--host dbhost\tDatabase server host name\n");
- print("\t-P/--port dbport\tDatabase server port (optional)\n");
- print("\t-u/--user dbuser\tDatabase user name\n");
- print("\t-p/--pass dbpass\tUser password (optional)\n");
- print("\t-d/--name dbname\tDatabase name (optional)\n");
- print("\t-?/--help\t\tDisplays this information\n");
-} ## end sub usage
-
-#-----------------------------------------------------------------------
-
-my $dryrun;
-my ( $dbhost, $dbport );
-my ( $dbuser, $dbpass );
-my $dbname;
-
-if (
- !GetOptions(
- 'dryrun|n' => \$dryrun,
- 'dbhost|host|h=s' => \$dbhost,
- 'dbport|port|P=i' => \$dbport,
- 'dbuser|user|u=s' => \$dbuser,
- 'dbpass|pass|p=s' => \$dbpass,
- 'dbname|name|d=s' => \$dbname,
- 'help|?' => sub { usage(); exit } )
- || !defined($dbhost)
- || !defined($dbuser) )
-{
- usage();
- exit;
-}
-
-my $registry = 'Bio::EnsEMBL::Registry';
-
-$registry->load_registry_from_db(
- '-host' => $dbhost,
- '-port' => $dbport,
- '-user' => $dbuser,
- '-pass' => $dbpass,
-);
-
-my $select_stmt = qq(
-SELECT DISTINCT LCASE(meta_value)
-FROM meta
-WHERE meta_key IN (
- 'species.taxonomy_id',
- 'species.common_name',
- 'species.ensembl_common_name',
- 'species.ensembl_alias_name'
-)
- AND species_id = 1
-);
-
-my $select_aliases_stmt = qq(
-SELECT DISTINCT LCASE(meta_value)
-FROM meta
-WHERE meta_key = 'species.alias'
- AND species_id = 1
-);
-
-my @dbas = @{ $registry->get_all_DBAdaptors( '-group' => 'Core' ) };
-
-foreach my $dba ( sort { $a->species() cmp $b->species() } @dbas ) {
- my $dbh = $dba->dbc()->db_handle();
- if ( defined($dbname) && $dbname ne $dba->dbc()->dbname() ) { next }
-
- my $species = $dba->species();
- if ( $species =~ /^Ancestral/ ) { next }
-
- printf( "%s{ %s }--\n",
- '-' x ( 80 - ( 6 + length($species) ) ), $species );
- printf( "Database = %s\n", $dba->dbc()->dbname() );
-
- my %automatic_aliases;
- my @existing_aliases;
-
- my $alias = $species;
- $automatic_aliases{$alias} = 1;
-
- $alias =~ tr [_] [ ];
- $automatic_aliases{$alias} = 1;
-
- $species =~ /^(.)[^_]*_(.*)$/;
- $alias = $1 . $2;
- $automatic_aliases{$alias} = 1;
-
- $species =~ /^(.)[^_]*_(...).*$/;
- $alias = $1 . $2;
- $automatic_aliases{$alias} = 1;
-
- $species =~ /^(...)[^_]*_(...).*$/;
- $alias = $1 . $2;
- $automatic_aliases{$alias} = 1;
-
- {
- my $select_sth = $dbh->prepare($select_stmt);
-
- $select_sth->execute();
-
- my $meta_value;
-
- $select_sth->bind_columns( \$meta_value );
-
- while ( $select_sth->fetch() ) {
- $automatic_aliases{$meta_value} = 1;
- }
- }
- {
- my $select_sth = $dbh->prepare($select_aliases_stmt);
-
- $select_sth->execute();
-
- my $meta_value;
-
- $select_sth->bind_columns( \$meta_value );
-
- while ( $select_sth->fetch() ) {
- push( @existing_aliases, $meta_value );
- }
- }
-
- my @old_aliases;
- print("Aliases =\n");
- foreach my $existing_alias ( sort(@existing_aliases) ) {
- if ( exists( $automatic_aliases{$existing_alias} ) ) {
- printf( "\t'%s' (automatic, in database)\n", $existing_alias );
- push( @old_aliases, $existing_alias );
- } else {
- printf( "\t'%s' (in database)\n", $existing_alias );
- }
- }
-
- map { delete( $automatic_aliases{$_} ) } @old_aliases;
-
- my @new_aliases =
- sort { length($a) <=> length($b) || $a cmp $b }
- keys(%automatic_aliases);
-
- if (@new_aliases) {
- foreach my $new_alias (@new_aliases) {
- printf( "\t'%s' (new automatic alias)\n", $new_alias );
- }
-
- my $insert_stmt = sprintf(
- "INSERT IGNORE INTO meta (species_id, meta_key, meta_value) "
- . "VALUES %s",
- join(
- ', ',
- map {
- sprintf( "( 1, 'species.alias', %s )", $dbh->quote( lc($_) ) )
- } @new_aliases
- ) );
-
- if ( !$dryrun ) {
- # Insert new aliases.
- $dbh->do($insert_stmt);
- print("Status = wrote new aliases to database\n");
- } else {
- print("Status = dry-run, not writing to database\n");
- }
- } else {
- print("Status = no new aliases to write to database\n");
- }
-
-} ## end foreach my $dba ( sort { $a...})