make sure if we use clone name for the gene name that we only get each clone...

make sure if we use clone name for the gene name that we only get each clone anem once, else add -201 at the end and increment for each one.

misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm

@@ -5915,6 +5915,58 @@ FSQL
   print "Uploading data in $object_xref_file to object_xref\n";
   $sth->execute() || die "error loading file $object_xref_file\n";
   
+
+#
+# Now check for duplicate clone names as gene names.
+#
+  
+  my $clone_file =  $self->core->dir()."/clone_names.sql";
+  
+  open(CLONE, ">$xref_file" ) || die "Could not open file $xref_file";
+
+  my $xref_list_sql = 'select x.xref_id, x.dbprimary_acc from external_db e, xref x, gene g, gene_stable_id gsi where e.external_db_id =x.external_db_id and e.db_name like "Clone_based_ensembl_gene" and g.gene_id = gsi.gene_id and g.display_xref_id = x.xref_id and x.display_label = ? order by gsi.stable_id';
+  
+  my $gene_list_sql = 'SELECT DISTINCT(x.display_label), COUNT(*) AS count FROM gene g, xref x, external_db e WHERE e.external_db_id=x.external_db_id AND g.biotype = "protein_coding" AND x.xref_id=g.display_xref_id and e.db_name like "Clone_based_ensembl_gene" GROUP BY x.display_label, e.db_name HAVING COUNT > 1';
+  
+
+  my @xref_name_list;
+  
+  
+  $sth = $self->core->dbc->prepare($gene_list_sql);
+  
+  $sth->execute();
+  my ($xref_label, $count);
+  $sth->bind_columns(\$xref_label,\$count);
+  while($sth->fetch()){
+    push @xref_name_list, $xref_label;
+  }
+  $sth->finish;
+  
+  
+  
+  $sth = $self->core->dbc->prepare($xref_list_sql);
+  
+  foreach my $name (@xref_name_list){
+    my $count = 201;
+    $sth->execute($name);
+    $sth->bind_columns(\$xref_id,\$acc);
+    while($sth->fetch()){
+      my $new = $acc."-".$count;
+      print CLONE 'update xref set dbprimary_acc = "'.$new.'" where xref_id = '.$xref_id.";\n";
+      print CLONE 'update xref set display_label = "'.$new.'" where xref_id = '.$xref_id.";\n";
+      $count++;
+    }
+  }
+  $sth->finish;
+  close CLONE;
+
+  my $mysql_command = $self->get_mysql_command($self->core->dbc);  
+
+  # Load the new clone xrefs from the appropriate file
+  system( "$mysql_command < $clone_file" ) == 0 
+    or print( "ERROR: parsing $clone_file in mysql\n" );
+
+
 }