diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
new file mode 100644
index 0000000000000000000000000000000000000000..5727910366423309013938fad819cd08a77ea11c
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -0,0 +1,214 @@
+package BasicMapper;
+
+use strict;
+use DBI;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+
+
+sub new {
+ my($class, $species, $host, $port, $dbname, $user, $password ,$dir) = @_;
+
+ my $self ={};
+ bless $self,$class;
+
+ $self->species($species);
+ $self->host($host);
+ $self->port($port);
+ $self->dbname($dbname);
+ $self->$user($user);
+ $self->$password($password);
+ $self->$dir($dir);
+}
+
+
+sub dump_seqs{
+ my ($self, $slice) = @_;
+ $self->dump_ensembl($slice);
+ $self->dump_xref();
+}
+
+
+sub dump_xref{
+ my ($self) = @_;
+
+
+ my $sql = "select species_id from species where name = '".$self->species."'";
+ my $sth = dbi()->prepare($sql);
+ $sth->execute();
+ my @row = $sth->fetchrow_array();
+ my $species_id;
+ if (defined @row) {
+ $species_id = $row[0];
+ } else {
+ print STDERR "Couldn't get ID for species ".$self->species."\n";
+ print STDERR "It must be one of :-\n";
+ $sql = "select name from species";
+ $sth = dbi()->prepare($sql);
+ $sth->execute();
+ while(my @row = $sth->fetchrow_array()){
+ print STDERR $row[0]."\n";
+ }
+ die("Please try again\n");
+ }
+
+
+ open(XDNA,">".$self->dir."/xref_dna.fasta") || die "Could not open xref_dna.fasta";
+ my $sql = "select p.xref_id, p.sequence from primary_xref p, xref x ";
+ $sql .= "where p.xref_id = x.xref_id and ";
+ $sql .= " p.sequence_type ='dna' and ";
+ $sql .= " x.species_id = ".$species_id." ";
+ $sth = dbi()->prepare($sql);
+ $sth->execute();
+ while(my @row = $sth->fetchrow_array()){
+ $row[1] =~ s/(.{60})/$1\n/g;
+ print XDNA ">".$row[0]."\n".$row[1]."\n";
+ }
+ close XDNA;
+
+ open(XPEP,">".$self->dir."/xref_prot.fasta") || die "Could not open xref_prot.fasta";
+ $sql = "select p.xref_id, p.sequence from primary_xref p, xref x ";
+ $sql .= "where p.xref_id = x.xref_id and ";
+ $sql .= " p.sequence_type ='peptide' and ";
+ $sql .= " x.species_id = ".$species_id." ";
+ $sth = dbi()->prepare($sql);
+ $sth->execute();
+ while(my @row = $sth->fetchrow_array()){
+ $row[1] =~ s/(.{60})/$1\n/g;
+ print XPEP ">".$row[0]."\n".$row[1]."\n";
+ }
+ close XPEP;
+
+}
+
+
+sub dump_ensembl{
+ my ($self) = @_;
+
+ #create filename
+ $self->ensembl_protein_file($self->dir."/".$self->species."_protein.fasta");
+ $self->ensembl_dna_file($self->dir."/".$self->species."_dna.fasta");
+
+
+ $self->fetch_and_dump_seq();
+
+}
+
+
+sub fetch_and_dump_seq{
+ my ($self, $type, $adaptortype) = @_;
+
+ my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-species => $self->species(),
+ -dbname => $self->dbname(),
+ -host => $self->host(),
+ -port => $self->port(),
+ -password => $self->password(),
+ -username => $self->username(),
+ -group => 'core');
+
+ open(FILE,">".$self->ensembl_dna_file())
+ || die("Could not open dna file for writing: ".$self->ensembl_dna_file."\n");
+
+ $gene_adap = $reg->get_adaptor($self->species(),'core','Gene');
+ my @genes = @{$gene_adap->list_dbIDs()};
+ foreach my $gene (@genes){
+ foreach my $transcript (@{$gene->get_all_Transcripts()}) {
+ my $seq = $transcript->spliced_seq();
+ $seq =~ s/(.{60})/$1\n/g;
+ print FILE ">" . $transcript->dbID() . "\n" .$seq."\n";
+ }
+ }
+ close FILE;
+
+ #now do the translations.
+
+}
+
+
+
+# @transcript_ids = @{$transcript_adaptor->list_dbIDs()};
+# $transcript = $transcript_adaptor->fetch_by_dbID($trans_id);
+
+
+
+# $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
+# $slice_adaptor = $db->get_SliceAdaptor();
+#
+# $transcript_adaptor = $db->get_TranscriptAdaptor();
+#
+# $transcript = $transcript_adaptor->fetch_by_dbID(1234);
+#
+# $transcript = $transcript_adaptor->fetch_by_stable_id('ENST00000201961');
+#
+# $slice = $slice_adaptor->fetch_by_region('chromosome', '3', 1, 1000000);
+# @transcripts = @{$transcript_adaptor->fetch_all_by_Slice($slice)};
+#
+# ($transcript) = @{$transcript_adaptor->fetch_all_by_external_name('BRCA2')};
+
+
+sub get_ensembl_type{
+
+ my %type; #
+
+ my $type{'Translation'} = "peptide";
+ $type{'Transcript'} = "dna";
+
+ return /%type;
+}
+
+sub species {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_species} = $arg );
+ return $self->{_species};
+}
+
+sub host {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_host} = $arg );
+ return $self->{_host};
+}
+
+
+sub port {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_port} = $arg );
+ return $self->{_port};
+}
+
+sub dbname {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_dbname} = $arg );
+ return $self->{_dbname};
+}
+
+sub user {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_user} = $arg );
+ return $self->{_user};
+}
+
+sub password {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_password} = $arg );
+ return $self->{_password};
+}
+
+sub dir {
+ my ($self, $arg) = @_;
+
+ (defined $arg) &&
+ ($self->{_dir} = $arg );
+ return $self->{_dir};
+}
+
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
new file mode 100644
index 0000000000000000000000000000000000000000..608fe52ffd51d78d0207f2cf7447aa46d6e7946f
--- /dev/null
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -0,0 +1,88 @@
+use strict;
+use warnings;
+
+use Getopt::Long;
+use Cwd;
+
+use vars qw(@INC);
+
+#effectively add this directory to the PERL5LIB automatically
+my $dir = cwd() . '/' . __FILE__;
+my @d = split(/\//, $dir);
+pop(@d);
+$dir = join('/', @d);
+unshift @INC, $dir;
+
+
+my ($file, $verbose, $help);
+
+GetOptions ('file=s' => \$file,
+ 'verbose' => \$verbose,
+ 'help' => sub { &show_help(); exit 1;} );
+
+usage("-file option is required") if(!$file);
+usage() if($help);
+
+open(FILE, $file) or die("Could not open input file '$file'");
+
+my @all_species;
+
+while( my $line = <FILE> ) {
+ chomp($line);
+ next if $line =~ /^#/;
+ next if !$line;
+
+ my ( $species, $host, $port, $dbname, $user, $password ,$dir) =
+ split( "\t", $line );
+
+ my $map;
+ eval "require XrefMapper::$species";
+ if($@) {
+ warn("Could not require mapper module XrefMapper::$species\n" .
+ "Using XrefMapper::BasicMapper instead:\n$@");
+ require XrefMapper::BasicMapper;
+ $species = "BasicMapper";
+ }
+
+ {
+ no strict 'refs';
+ $map = "XrefMapper::$species"->new
+ ( $species, $host, $port, $dbname, $user, $password ,$dir);
+
+ }
+
+ push @all_species, $map;
+
+}
+
+for my $species ( @all_species ) {
+ $species->dump_seqs();
+ $species->run_matching();
+ $species->store();
+}
+
+
+print STDERR "*** All finished ***\n";
+
+sub usage {
+ my $msg = shift;
+
+ print STDERR "$msg\n\n" if($msg);
+ print STDERR <<EOF;
+usage: perl xref_mapper <options>
+
+options: -file <input_file> input file with tab delimited 'species',
+ 'host', 'port', 'dbname' ,'user', 'password' and 'directory'
+ values on each line
+
+ -verbose print out debug statements
+
+ -help display this message
+
+example: perl xref_mapper.pl -file mapper.input \\
+ -verbose
+
+EOF
+
+ exit;
+}