NOT ready yet just making sure i have safe copy for now

misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm

+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};
+}
+ 

misc-scripts/xref_mapping/xref_mapper.pl

+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;
+}