Attach SGD mapping to translation object rather than transcript objects, so GO...

Attach SGD mapping to translation object rather than transcript objects, so GO mapping get also attach to translations. Commented STDERR statements;

misc-scripts/xref_mapping/XrefParser/SGDParser.pm

@@ -27,7 +27,8 @@ sub run {
   my $file = @{$files}[0];
 
   my $gene_source_id = $self->get_source_id_for_source_name("SGD_GENE");
-  my $transcript_source_id = $self->get_source_id_for_source_name("SGD_TRANSCRIPT");
+  #my $transcript_source_id = $self->get_source_id_for_source_name("SGD_TRANSCRIPT");
+  my $translation_source_id = $self->get_source_id_for_source_name("SGD_TRANSLATION");
 
   my $sgd_io = $self->get_filehandle($file);
 
@@ -52,9 +53,9 @@ sub run {
 	if ($biotype =~ /ORF|.+RNA|transposable_element_gene|pseudogene/) {
 
 	    if ($verbose) {
-		print STDERR "parsing line for biotype, $biotype\n";
-		print STDERR "sgd_id, biotype, status, orf_name, locus_name, alias_name, $sgd_id, $biotype, $status, $orf_name, $locus_name, $alias_name\n";
-		print STDERR "desc: $desc\n";
+		#print STDERR "parsing line for biotype, $biotype\n";
+		#print STDERR "sgd_id, biotype, status, orf_name, locus_name, alias_name, $sgd_id, $biotype, $status, $orf_name, $locus_name, $alias_name\n";
+		#print STDERR "desc: $desc\n";
 	    }
 
 	    if (!defined $locus_name || ($locus_name eq "")) {
@@ -64,7 +65,7 @@ sub run {
 		}
 		else {
 		    if ($verbose) {
-			print STDERR "assigning the orf_name as the locus_name(ie the gene_name)\n";
+			#print STDERR "assigning the orf_name as the locus_name(ie the gene_name)\n";
 		    }
 		    $locus_name = $orf_name;
 		}
@@ -78,23 +79,21 @@ sub run {
 						 source_id  => $gene_source_id,
 						 species_id => $species_id,
 						 info_type  => "DIRECT"} );
-
 	    $self->add_direct_xref($gene_xref_id, $orf_name, "Gene", "DIRECT");
 
-	    my $transcript_xref_id = $self->add_xref({ acc        => $sgd_id,
-						       label      => $locus_name,
-						       desc       => $desc,
-						       source_id  => $transcript_source_id,
-						       species_id => $species_id,
-						       info_type  => "DIRECT"} );
-
-	    $self->add_direct_xref($transcript_xref_id, $orf_name, "Transcript", "DIRECT");
+	    my $translation_xref_id = $self->add_xref({ acc        => $sgd_id,
+			 			        label      => $locus_name,
+						        desc       => $desc,
+						        source_id  => $translation_source_id,
+						        species_id => $species_id,
+						        info_type  => "DIRECT"} );
+	    $self->add_direct_xref($translation_xref_id, $orf_name, "Translation", "DIRECT");
 
 	    $xref_count++;
 
 	    foreach my $synonym (@syn){
 		if ($verbose) {
-		    print STDERR "adding synonym, $synonym\n";
+		    # print STDERR "adding synonym, $synonym\n";
 		}
 		$self->add_to_syn($sgd_id, $gene_source_id, $synonym, $species_id);
 		$syn_count++;
@@ -103,7 +102,7 @@ sub run {
 	}
 	else {
 	    if ($verbose) {
-		print STDERR "filtering biotype, $biotype\n";
+		#print STDERR "filtering biotype, $biotype\n";
 	    }
 	}
     }