Fix to xref output duplicate filtering.

misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm

@@ -926,6 +926,10 @@ sub dump_core_xrefs {
   # execute several queries with a max of 200 entries in each IN clause - more efficient
   my $batch_size = 200;
 
+  # keep track of what xref_ids have been written to prevent duplicates; e.g. several dependent
+  # xrefs my be dependent on the same master xref.
+  my %xrefs_written;
+
   while(@xref_ids) {
 
     my @ids;
@@ -950,20 +954,17 @@ sub dump_core_xrefs {
     my ($xref_id, $accession, $version, $label, $description, $source_id, $species_id, $master_xref_id);
     $xref_sth->bind_columns(\$xref_id, \$accession, \$version, \$label, \$description, \$source_id, \$species_id);
 
-    # keep track of what xref_ids have been written to prevent duplicates; e.g. several dependent
-    # xrefs my be dependent on the same master xref.
-    my %xrefs_written;
-
     # note the xref_id we write to the file is NOT the one we've just read
     # from the internal xref database as the ID may already exist in the
     # core database so we add on $xref_id_offset
     while ($xref_sth->fetch()) {
 
-      my $external_db_id = $source_to_external_db{$source_id};
-      print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
-      $xrefs_written{$xref_id} = 1;
-      $source_ids{$source_id} = $source_id;
-
+      if (!$xrefs_written{$xref_id}) {
+	my $external_db_id = $source_to_external_db{$source_id};
+	print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
+	$xrefs_written{$xref_id} = 1;
+	$source_ids{$source_id} = $source_id;
+      }
     }
 
     # Now get the dependent xrefs for each of these xrefs and write them as well