my $self = shift;
	$self->debug ("Patching gene, transcript, gene_description and external_db tables back to sch-30");
	my $target = $self->target;
	my $dbh = $self->dbh;
	$dbh->do("DROP TABLE $target.gene");
	$dbh->do( qq(CREATE TABLE $target.gene (
                 `gene_id` int(10) unsigned NOT NULL auto_increment,
                 `type` varchar(40) NOT NULL default '',
                 `analysis_id` int(11) default NULL,
                 `seq_region_id` int(10) unsigned NOT NULL default '0',
                 `seq_region_start` int(10) unsigned NOT NULL default '0',
                 `seq_region_end` int(10) unsigned NOT NULL default '0',
                 `seq_region_strand` tinyint(2) NOT NULL default '0',
                 `display_xref_id` int(10) unsigned default NULL,
                  PRIMARY KEY  (`gene_id`),
                  KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
                  KEY `xref_id_index` (`display_xref_id`),
                  KEY `analysis_idx` (`analysis_id`)
                  ) ENGINE=MyISAM DEFAULT CHARSET=latin1
                ));
	$dbh->do("DROP TABLE $target.transcript");
	$dbh->do( qq(CREATE TABLE $target.transcript (
                 `transcript_id` int(10) unsigned NOT NULL auto_increment,
                 `gene_id` int(10) unsigned NOT NULL default '0',
                 `seq_region_id` int(10) unsigned NOT NULL default '0',
                 `seq_region_start` int(10) unsigned NOT NULL default '0',
                 `seq_region_end` int(10) unsigned NOT NULL default '0',
                 `seq_region_strand` tinyint(2) NOT NULL default '0',
                 `display_xref_id` int(10) unsigned default NULL,
                 PRIMARY KEY  (`transcript_id`),
                 KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
                 KEY `gene_index` (`gene_id`),
                 KEY `xref_id_index` (`display_xref_id`)
                 ) ENGINE=MyISAM DEFAULT CHARSET=latin1
                ));
	$dbh->do( qq(CREATE TABLE $target.gene_description (
                 `gene_id` int(10) unsigned NOT NULL default '0',
                 `description` text,
                 PRIMARY KEY  (`gene_id`)
                 ) ENGINE=MyISAM DEFAULT CHARSET=latin1
                ));
	$dbh->do("DROP TABLE $target.external_db");
	$dbh->do( qq(CREATE TABLE $target.external_db (
                 `external_db_id` int(11) NOT NULL default '0',
                 `db_name` varchar(100) NOT NULL default '',
                 `release` varchar(40) NOT NULL default '',
                 `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL default 'KNOWNXREF',
                 PRIMARY KEY  (`external_db_id`)
                 ) ENGINE=MyISAM DEFAULT CHARSET=latin1
                ));

    my $self = shift;

    # copy assembly_exception table
    $self->debug('Vega specific - copying assembly_exception table');
    $self->copy_tables('assembly_exception');

    my $source = $self->source();
    my $target = $self->target();
    my $dbh    = $self->dbh();

    # fix seq_region_id in assembly_exception
    $self->debug('Vega specific - Updating seq_region_id in assembly_exception table');
    $dbh->do(qq(
        UPDATE $target.assembly_exception, $target.tmp_chr_map
        SET assembly_exception.seq_region_id = tmp_chr_map.new_id
        WHERE assembly_exception.seq_region_id = tmp_chr_map.old_id
    ));
    $dbh->do(qq(
        UPDATE $target.assembly_exception, $target.tmp_chr_map
        SET assembly_exception.exc_seq_region_id = tmp_chr_map.new_id
        WHERE assembly_exception.exc_seq_region_id = tmp_chr_map.old_id
    ));

    # fix seq_region.length if necessary (this is the case if you have an
    # assembly_exception at the end of a chromosome)
    my $sth1 = $dbh->prepare(qq(
        UPDATE $target.seq_region SET length = ? WHERE seq_region_id = ?
    ));
    my $sth2 = $dbh->prepare(qq(
        SELECT
                sr.seq_region_id,
                sr.length,
                max(ae.seq_region_end)
        FROM
                $target.seq_region sr,
                $target.assembly_exception ae
        WHERE   sr.seq_region_id = ae.seq_region_id
        GROUP BY ae.seq_region_id
    ));
    $sth2->execute;
    while (my ($sr_id, $sr_length, $max_ae_length) = $sth2->fetchrow_array) {
        if ($max_ae_length > $sr_length) {
            $self->debug("  Updating seq_region.length for $sr_id (old $sr_length, new $max_ae_length)");
            $sth1->execute($max_ae_length, $sr_id);
        }
    }
}

# reset gene, transcript, gene_description and external_db tables back to 30

    my $self=shift;
    my $source = $self->source();
    my $target = $self->target();
    my $sth = $self->dbh()->prepare
        ("INSERT INTO $target.current_clone_info(clone_id,clone_info_id) SELECT * FROM $source.current_clone_info");
    $sth->execute();
    $sth->finish();

    my $self = shift;
    return;

    my $self = shift;
    $self->copy_tables(
        # vega tables
        "gene_synonym",
        "transcript_info",
        "current_gene_info",
        "current_transcript_info",
        "author",
        "gene_name",
        "transcript_class",
        "gene_remark",
        "gene_info",
        "evidence",
        "transcript_remark",
        "clone_remark",
        "clone_info",
        "clone_info_keyword",
        "assembly_tag",
   );
    eval { $self->copy_current_clone_info; };
	warn $@ if $@;

    my $self = shift;
    
    my $target = $self->target();
    my $dbh    = $self->dbh();
    $self->debug("Vega specific - removing supercontigs from $target");

    $dbh->do("DELETE FROM $target.meta ". 
             "WHERE meta_value like '%supercontig%'");

    $dbh->do("DELETE FROM $target.coord_system ".
             "WHERE name like 'supercontig'");
    
    $dbh->do("DELETE $target.a ".
             "FROM $target.assembly a, $target.seq_region sr ". 
             "WHERE sr.coord_system_id = 2 ".
             "and a.asm_seq_region_id = sr.seq_region_id");

    $dbh->do("DELETE FROM $target.seq_region ".
             "WHERE coord_system_id = 2");

    my $self = shift;
    return;