add more fields for GFF3 format

modules/Bio/EnsEMBL/Exon.pm

@@ -1595,6 +1595,7 @@ sub summary_as_hash {
   $summary_ref->{'constitutive'} = $self->is_constitutive;
   $summary_ref->{'ensembl_phase'} = $self->phase;
   $summary_ref->{'ensembl_end_phase'} = $self->end_phase;
+  $summary_ref->{'exon_id'} = $summary_ref->{'id'};
   return $summary_ref;
 }
 

modules/Bio/EnsEMBL/Feature.pm

@@ -1470,7 +1470,9 @@ sub get_nearest_Gene {
 sub summary_as_hash {
   my $self = shift;
   my %summary;
-  $summary{'id'} = $self->display_id;
+  my $id = $self->display_id;
+  if ($self->version()) { $id .= "." . $self->version(); }
+  $summary{'id'} = $id;
   $summary{'version'} = $self->version() if $self->version();
   $summary{'start'} = $self->seq_region_start;
   $summary{'end'} = $self->seq_region_end;

modules/Bio/EnsEMBL/Gene.pm

@@ -1482,6 +1482,7 @@ sub summary_as_hash {
   $summary_ref->{'Name'} = $self->external_name if $self->external_name;
   $summary_ref->{'logic_name'} = $self->analysis->logic_name();
   $summary_ref->{'source'} = $self->source();
+  $summary_ref->{'gene_id'} = $summary_ref->{'id'};
   return $summary_ref;
 }
 

modules/Bio/EnsEMBL/Transcript.pm

@@ -3051,9 +3051,44 @@ sub summary_as_hash {
   my $parent_gene = $self->get_Gene();
   $summary_ref->{'Parent'} = $parent_gene->stable_id;
   $summary_ref->{'source'} = $parent_gene->source();
+  $summary_ref->{'transcript_id'} = $summary_ref->{'id'};
+  $summary_ref->{'havana_transcript'} = $self->havana_transcript->display_id() if $self->havana_transcript();
+  $summary_ref->{'ccdsid'} = $self->ccds->display_id() if $self->ccds();
   return $summary_ref;
 }
 
+=head2 havana_transcript
+
+  Example       : $havana_transcript = $transcript->havana_transcript();
+  Description   : Locates the corresponding havana transcript
+  Returns       : Bio::EnsEMBL::DBEntry
+=cut
+
+sub havana_transcript {
+  my $self = shift;
+  my @otts = @{ $self->get_all_DBEntries('OTTT') };
+  my $ott;
+  $ott = $otts[0] if scalar(@otts) > 0;
+  return $ott;
+}
+
+=head2 ccds
+
+  Example       : $ccds = $transcript->ccds();
+  Description   : Locates the corresponding ccds xref
+  Returns       : Bio::EnsEMBL::DBEntry
+=cut
+
+sub ccds {
+  my $self = shift;
+  my @ccds = @{ $self->get_all_DBEntries('CCDS') };
+  my $ccds;
+  $ccds = $ccds[0] if scalar(@ccds) > 0;
+  return $ccds;
+}
+
+
+
 =head2 get_Gene
   
   Example     : $gene = $transcript->get_Gene;

modules/Bio/EnsEMBL/Translation.pm

@@ -1233,7 +1233,10 @@ sub get_all_DAS_Features{
 sub summary_as_hash {
   my $self = shift;
   my %summary;
-  $summary{'id'} = $self->display_id;
+  my $id = $self->display_id;
+  if ($self->version) { $id .= "." . $self->version; }
+  $summary{'id'} = $id;
+  $summary{'protein_id'} = $id;
   $summary{'genomic_start'} = $self->genomic_start;
   $summary{'genomic_end'} = $self->genomic_end;
   $summary{'length'} = $self->length;

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

@@ -205,9 +205,8 @@ sub print_feature {
         my @ordered_values = @summary{@ordered_keys};
         while (my $key = shift @ordered_keys) {
             my $value = shift @ordered_values;
-            delete $summary{$key};
             if ($value && $value ne '') {
-                if ($key eq 'id') {
+                if ($key =~ /id/) {
                   if ($feature->isa('Bio::EnsEMBL::Transcript')) {
                     $value = 'transcript:' . $value;
                   } elsif ($feature->isa('Bio::EnsEMBL::Gene')) {
@@ -217,6 +216,8 @@ sub print_feature {
                   } else {
                     $value = $so_term . ':' . $value;
                   }
+                } else {
+                  delete $summary{$key};
                 }
                 if ($key eq 'Parent') {
                  if ($feature->isa('Bio::EnsEMBL::Transcript')) {