fixes to serializer sample scripts

scripts/gff3_serializer.pl

@@ -8,18 +8,18 @@
 # Dumper chromosome 1 only for size/speed, takes about 20 minutes
 #
 
-$|++;
-
 use strict;
 use warnings;
 use Data::Dumper;
 use Getopt::Long;
 
 use Bio::EnsEMBL::Registry;
-use Bio::EnsEMBL::IO::Translator::EnsFeature;
+use Bio::EnsEMBL::IO::Translator::Feature;
 use Bio::EnsEMBL::IO::Writer::GFF3;
 use Bio::EnsEMBL::IO::Object::GXFMetadata;
 
+$|++;
+
 my $dbhost = 'ensembldb.ensembl.org';
 my $dbuser = 'anonymous';
 my $dbpass;
@@ -50,7 +50,7 @@ my $adaptor = Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "Slice" );
 my $ga = Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "Gene" );
 my $dba = $adaptor->db();
 
-my $translator = Bio::EnsEMBL::IO::Translator::EnsFeature->new();
+my $translator = Bio::EnsEMBL::IO::Translator::Feature->new();
 my $serializer = Bio::EnsEMBL::IO::Writer::GFF3->new($translator);
 $serializer->open($outfile);
 
@@ -116,7 +116,7 @@ while(my $chromosome = shift @{$features}) {
     $serializer->write($chromosome);
 
     # Write out the end of section separator for the GFF3 (ie. ###)
-    $serializer->fwd_ref_delimeter();
+    # $serializer->fwd_ref_delimeter();
 
     # Cycle through and print chromosomes, depends on DB ordering, not likely
     # good for production
@@ -143,7 +143,7 @@ while(my $chromosome = shift @{$features}) {
 	}
 
 	# Write out the end of section separator for the GFF3 (ie. ###)
-	$serializer->fwd_ref_delimeter();
+	# $serializer->fwd_ref_delimeter();
 
     }
 }

scripts/gtf_serializer.pl

@@ -8,19 +8,19 @@
 # Dumper chromosome 1 only for size/speed, takes about 20 minutes
 #
 
-$|++;
-
 use strict;
 use warnings;
 use Data::Dumper;
 use Getopt::Long;
 
 use Bio::EnsEMBL::Registry;
-use Bio::EnsEMBL::IO::Translator::EnsFeature;
+use Bio::EnsEMBL::IO::Translator::Feature;
 use Bio::EnsEMBL::IO::Writer::GTF;
 use Bio::EnsEMBL::IO::Object::GXFMetadata;
 use Bio::EnsEMBL::IO::Object::GTF;
 
+$|++;
+
 my $dbhost = 'ensembldb.ensembl.org';
 my $dbuser = 'anonymous';
 my $dbpass;
@@ -51,7 +51,7 @@ my $adaptor = Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "Slice" );
 my $ga = Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "Gene" );
 my $dba = $adaptor->db();
 
-my $translator = Bio::EnsEMBL::IO::Translator::EnsFeature->new();
+my $translator = Bio::EnsEMBL::IO::Translator::Feature->new();
 my $serializer = Bio::EnsEMBL::IO::Writer::GTF->new($translator);
 
 # Two ways to override the callback table

scripts/vcf4_serializer.pl

@@ -3,8 +3,6 @@
 # Sample VCF4 serializer using the new ensembl-io methodology.
 #
 
-$|++;
-
 use strict;
 use warnings;
 #use Data::Dumper;
@@ -14,6 +12,8 @@ use Bio::EnsEMBL::IO::Translator::SampleGenotypeFeature;
 use Bio::EnsEMBL::IO::Writer::VCF4;
 use Bio::EnsEMBL::IO::Object::VCF4Metadata;
 
+$|++;
+
 my $db_version = Bio::EnsEMBL::ApiVersion->software_version;
 
 # Connect to the Ensembl Registry to access the databases

scripts/vcf4_sv_serializer.pl

@@ -3,8 +3,6 @@
 # Sample VCF4 serializer using the new ensembl-io methodology.
 #
 
-$|++;
-
 use strict;
 use warnings;
 #use Data::Dumper;
@@ -14,6 +12,8 @@ use Bio::EnsEMBL::IO::Translator::StructuralVariationFeature;
 use Bio::EnsEMBL::IO::Writer::VCF4;
 use Bio::EnsEMBL::IO::Object::VCF4Metadata;
 
+$|++;
+
 my $db_version = Bio::EnsEMBL::ApiVersion->software_version;
 
 # Connect to the Ensembl Registry to access the databases