update to gff3 output format:

- for ID field, concatenate object type before the stable id
- if gene biotype is protein_coding, the so term is replaced by gene

modules/Bio/EnsEMBL/Utils/IO/GFFSerializer.pm

@@ -124,6 +124,10 @@ sub print_feature {
 #   Column 3 - feature, the ontology term for the kind of feature this row is
 	my $so_term = eval { $so_mapper->to_name($feature); };
 	$@ and throw sprintf "Unable to map feature %s to SO term.\n$@", $summary{ID};
+        if ($so_term eq 'protein_coding_gene') { 
+# Special treatment for protein_coding_gene, as more commonly expected term is 'gene'
+          $so_term = 'gene';
+        }
         $row .= $so_term."\t";
 
 #    Column 4 - start, the start coordinate of the feature, here shifted to chromosomal coordinates
@@ -137,6 +141,14 @@ sub print_feature {
             # non-circular, but end still before start
             else {$summary{'end'} = $summary{'start'};}
         }
+        if ($feature->slice()) {
+          if ($summary{'start'} < $feature->slice->start()) {
+            $summary{'start'} = $feature->slice->start();
+          }
+          if ($summary{'end'} > $feature->slice->end()) {
+            $summary{'end'} = $feature->slice->end();
+          }
+        }
         $row .= $summary{'start'} . "\t";
 
 #    Column 5 - end, coordinates (absolute) for the end of this feature
@@ -173,6 +185,7 @@ sub print_feature {
         delete $summary{'start'};
         delete $summary{'end'};
         delete $summary{'strand'};
+        delete $summary{'phase'};
         delete $summary{'score'};
         delete $summary{'source'};
 #   Slice the hash for specific keys in GFF-friendly order
@@ -181,6 +194,24 @@ sub print_feature {
         while (my $key = shift @ordered_keys) {
             my $value = shift @ordered_values;
             if ($value) {
+                if ($key eq 'ID') {
+                  if ($feature->isa('Bio::EnsEMBL::Transcript')) {
+                    $value = 'transcript:' . $value;
+                  } elsif ($feature->isa('Bio::EnsEMBL::Gene')) {
+                    $value = 'gene:' . $value;
+                  } else {
+                    $value = $so_term . ':' . $value;
+                  }
+                }
+                if ($key eq 'Parent') {
+                 if ($feature->isa('Bio::EnsEMBL::Transcript')) {
+                    $value = 'gene:' . $value;
+                  } elsif ($feature->isa('Bio::EnsEMBL::Exon')) {
+                    $value = 'transcript:' . $value;
+                  } elsif ($so_term eq 'CDS') {
+                    $value = 'transcript:' . $value;
+                  }
+                }
                 $row .= $key."=".uri_escape($value,'\t\n\r;=%&,');
                 delete $summary{$key};
                 $row .= ';' if scalar(@ordered_keys) > 0 || scalar(keys %summary) > 0;
@@ -195,7 +226,7 @@ sub print_feature {
                 $data_written = 1;
             }
             else {
-                if ($summary{$attribute}) { 
+                if (defined $summary{$attribute}) { 
                   $row .= $attribute."=".uri_escape($summary{$attribute},'\t\n\r;=%&,'); 
                   $data_written = 1;
                 }