Very basic gff serialiser test

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

@@ -41,6 +41,7 @@ use Bio::EnsEMBL::Utils::Exception;
 use Bio::EnsEMBL::Utils::BiotypeMapper;
 use URI::Escape;
 use Bio::EnsEMBL::Utils::IO::FeatureSerializer;
+use Bio::EnsEMBL::Utils::Scalar qw/check_ref/;
 
 use base qw(Bio::EnsEMBL::Utils::IO::FeatureSerializer);
 
@@ -63,7 +64,7 @@ sub new {
         filehandle => shift,
     };
     bless $self, $class;
-    if ( ref($self->{'ontology_adaptor'}) ne "Bio::EnsEMBL::DBSQL::OntologyTermAdaptor" ) {
+    if ( ! check_ref($self->{'ontology_adaptor'}, "Bio::EnsEMBL::DBSQL::OntologyTermAdaptor" )) {
         throw("GFF format requires an instance of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor to function. See also Bio::EnsEMBL::Utils::BiotypeMapper");        
     }
     $self->{'mapper'} = new Bio::EnsEMBL::Utils::BiotypeMapper($self->{'ontology_adaptor'});

modules/t/gffSerialiser.t

+package Test::SO::Term;
+
+sub new {
+  my ($class) = @_;
+  return bless({}, ref($class) || $class);
+}
+
+sub name {
+  my ($self) = @_;
+  return 'feature';
+}
+
+package Test::SO;
+
+use base qw/Bio::EnsEMBL::DBSQL::OntologyTermAdaptor/;
+
+sub new {
+  my ($class) = @_;
+  return bless({}, ref($class) || $class);
+}
+
+sub fetch_by_accession {
+  my ($self) = @_;
+  return Test::SO::Term->new();
+}
+
+package main;
+
+use strict;
+use warnings;
+use Test::More;
+use Bio::EnsEMBL::Test::MultiTestDB;
+use Bio::EnsEMBL::Utils::IO::GFFSerializer;
+use IO::String;
+
+my $db = Bio::EnsEMBL::Test::MultiTestDB->new();
+my $dba = $db->get_DBAdaptor('core');
+
+my $id = 'ENSG00000131044';
+
+my $ga = $dba->get_GeneAdaptor();
+my $gene = $ga->fetch_by_stable_id($id);
+
+{
+  my $ota = Test::SO->new();
+  my $fh = IO::String->new();
+  my $ser = Bio::EnsEMBL::Utils::IO::GFFSerializer->new($ota, $fh);
+  $ser->print_main_header([$gene->feature_Slice()]);
+  $ser->print_feature($gene);
+  
+  my $expected = <<'OUT';
+##gff-version 3
+##sequence-region   20 30274334 30300924
+OUT
+  #Have to do this outside of the HERETO thanks to tabs
+  $expected .= join("\t", 
+    qw/20  EnsEMBL feature 30274334  30300924  . + ./,
+    'ID=ENSG00000131044;logic_name=ensembl;external_name=C20orf125;description=DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474%2C ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL%3BAcc:Q9BR18];biotype=protein_coding' 
+  );
+  $expected .= "\n";
+
+  is(${$fh->string_ref()}, $expected, 'Gene serialises to GFF3 as expected');
+}
+
+done_testing();
\ No newline at end of file