removed go stuff from process_priority_xrefs as go xrefs cannot be priority...

removed go stuff from process_priority_xrefs as go xrefs cannot be priority xrefs. This is becouse with priority xrefs we just find the best match and ignore the others. For Go terms this is not appropriate as they should match many ensembl entries

misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm

@@ -1349,7 +1349,6 @@ PSQL
   my $object_xref_id =  $max_object_xref_id + 1;
   my @go_depend = ();
   open(XREF_P,">$dir/xref_priority.txt") || die "Could not open xref_priority.txt";
-  open(GO_XREF_P,">$dir/go_xref_priority.txt") || die "Could not open go_xref_priority.txt";
   open(OBJECT_XREF_P,">$dir/object_xref_priority.txt") || die "Could not open object_xref_priority.txt"; 
   open(IDENTITY_XREF_P,">$dir/identity_xref_priority.txt") || die "Could not open identity_xref_priority.txt";
   open(IDENTITY_XREF_TEMP,">>$dir/identity_xref_temp.txt") || die "Could not open identity_xref_temp.txt";
@@ -1393,36 +1392,11 @@ PSQL
 	print OBJECT_XREF_P $object_xref_id."\t".$id."\t".$type."\t".$dependent.
 	  "\tFROM:".$source_name.":".$acc."\n";	  
 	print IDENTITY_XREF_TEMP $object_xref_id."\t".$primary_identity{$xref_id}{$id."|".$type};
-#	print GO_XREF $object_xref_id . "\t" . $linkage_annotation . "\n"  if (defined($go_source{$source_id}));
-	
 	$object_xref_id++;	  
       }
     } 
   }
 
-  #
-  # special"GO" bit for go xrefs we need to add the linkage annotation.
-  #
-  my %go_xrefs = ();
-  if(values %priority_xref){
-    my $go_sql = "select master_xref_id, dependent_xref_id, linkage_annotation from dependent_xref where dependent_xref_id in (";
-    $go_sql .= join(", ", values %priority_xref).") AND linkage_annotation is not null";
-    
-    my $sth = $self->xref->dbc->prepare($go_sql) || die "prepare failed";
-    $sth->execute() || die "execute failed";
-    
-    my ($master_xref, $go_xref,$annot);
-    $sth->bind_columns(\$master_xref, \$go_xref,\$annot);
-    my $go_count=0;
-    while($sth->fetch()){
-      $go_count++;
-      $go_xrefs{$go_xref} = $annot;
-    }
-    print "THRERE ARE $go_count go xrefs\n";
-    $sth->finish;
-  }
-  
-
   foreach my $key (keys %priority_xref){
     my($source_name,$acc) = split(/:/,$key);
     my $xref_id = $priority_xref{$key};
@@ -1435,9 +1409,6 @@ PSQL
       my ($type,$id) = split(/:/,$priority_object_xref{$key});
       $object_succesfully_mapped{$xref_id} = 1;
       print OBJECT_XREF_P $object_xref_id."\t".$id."\t".$type."\t".($xref_id+$xref_id_offset)."\t\\N\n";
-      if(defined($go_xrefs{$xref_id})){
-	print GO_XREF_P  $object_xref_id."\t".$go_xrefs{$xref_id}."\n";
-      }
       if(defined($priority_identity_xref{$key})){
         print IDENTITY_XREF_P $object_xref_id."\t".$priority_identity_xref{$key};
       }
@@ -1478,7 +1449,6 @@ PSQL
   $sth->finish;
 
   close XREF_P;
-  close GO_XREF_P;
   close OBJECT_XREF_P;
   close IDENTITY_XREF_P;
   close IDENTITY_XREF_TEMP;