removed LRG section as it is not currently used

misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm

@@ -240,13 +240,6 @@ SQ0
 	$official_name_used{$gene_symbol_xref_id} = 1;
     }
 
-    ############################################
-    # If not found see if there is an LRG entry
-    ############################################
-    if(!defined($gene_symbol)){ # look for LRG
-      ($gene_symbol, $gene_symbol_xref_id) = $self->find_lrg_hgnc($gene_id);
-    }
-
     ####################################################
     # If not found look for other valid database sources
     # These are RFAM and miRBase, as well as Uniprot_genename
@@ -1171,89 +1164,6 @@ sub get_xref_id_for_gene_symbol{
   }
   return $xref_id;
 }
-########################## START LRG BIT ######################################################
-
-sub get_lrg_find_sth{
-  my $self = shift;
-  
-  if(!defined($self->{'_lrg_find_sth'})){
-    my $sql=(<<'SQ2');
-SELECT x.label, x.xref_id, ox.object_xref_id, s.priority 
-  FROM xref x, object_xref ox, source s 
-    WHERE x.xref_id = ox.xref_id AND
-          x.source_id = s.source_id AND 
-          s.name = ? AND
-          ox.ensembl_id = ? AND
-          ox.ensembl_object_type = ?
-SQ2
-   $self->{'_lrg_find_sth'} =$self->xref->dbc->prepare($sql);
-  }
-  return $self->{'_lrg_find_sth'};
-}
-
-
-sub get_lrg_set_status_sth{
-  my $self = shift;
-  
-  if(!defined($self->{'_lrg_set_status_sth'})){
-     $self->{'_lrg_set_status_sth'} =
-       $self->xref->dbc->prepare("update object_xref set ox_status = 'NO_DISPLAY' where object_xref_id = ?");
-  }
-  return $self->{'_lrg_set_status_sth'};
-}
-
-sub get_lrg_to_hgnc_sth{
-  my $self = shift;
-  
-  if(!defined($self->{'_lrg_to_hgnc_sth'})){
-    my $sql=(<<'SQ4');
-SELECT x.xref_id, s.priority 
-  FROM xref x,source s, object_xref ox
-    WHERE x.xref_id = ox.xref_id AND
-          x.source_id = s.source_id AND
-          x.label = ? AND
-          s.name = ? AND
-          ox.ox_status = 'DUMP_OUT'
-    ORDER BY s.priority
-SQ4
-   $self->{'_lrg_to_hgnc_sth'} = $self->xref->dbc->prepare($sql);
-  }
-  return $self->{'_lrg_to_hgnc_sth'};
-}
-
-
-sub find_lrg_hgnc{
-  my ($self, $gene_id) =@_;
-  my $gene_symbol;
-  my $gene_symbol_xref_id;
-
-  my $lrg_find_sth = $self->get_lrg_find_sth();
-  my $lrg_set_status_sth = $self->get_lrg_set_status_sth();
-  my $lrg_to_hgnc_sth = $self->get_lrg_to_hgnc_sth();
-
-  # look for LRG_HGNC_notransfer, if found then find HGNC equiv and set to this
-  #      print "LRG FOUND with no HGNC, should have gotten this via the alt allele table?? gene_id = $gene_id\n";
-  $lrg_find_sth->execute("LRG_HGNC_notransfer", $gene_id, "Gene");
-  my ($display, $xref_id, $object_xref_id, $level);
-  $lrg_find_sth->bind_columns(\$display, \$xref_id, \$object_xref_id, \$level);
-  while($lrg_find_sth->fetch){
-    $lrg_set_status_sth->execute($object_xref_id); # set oc_status to no _display as we do not want this transferred, 
-                                                   # just the equivalent hgnc
-    my $new_xref_id  = undef;
-    my $pp;
-    $lrg_to_hgnc_sth->execute($display,"HGNC");
-	$lrg_to_hgnc_sth->bind_columns(\$new_xref_id,\$pp);
-    $lrg_to_hgnc_sth->fetch;
-    if(defined($new_xref_id)){
-      $gene_symbol = $display;
-	  $gene_symbol_xref_id = $new_xref_id;
-    }
-  }
-  return ($gene_symbol, $gene_symbol_xref_id);
-}
-
-#############################END LRG BIT ################################################
-
 
 
 #