merging changes from branch-ensembl-68

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

@@ -23,11 +23,10 @@ Monika Komorowska, 2012 - monika@ebi.ac.uk
 
 use strict;
 use Bio::EnsEMBL::Utils::IO::GFFParser;
-use FileHandle;
+use IO::File;
 
 my $file_name = "features.gff";
-my $fh = FileHandle->new;
-$fh->open("< $file_name");
+my $fh = IO::File->new($file_name, 'r');
 my $parser = Bio::EnsEMBL::Utils::IO::GFFParser->new($fh);
 
 my @header_lines = @{$parser->parse_header()};

modules/t/MultiTestDB.conf.example

@@ -4,11 +4,16 @@
   'user'   => 'ensadmin',
   'pass'   => 'XXX',
   'host'   => 'ens-research',
-  'zip'    => 'test_genome.zip',
-
+  
   # add a line with the dbname and module
   'databases' => {
-    'homo_sapiens' => { 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor' }
+    'homo_sapiens' => { 
+      'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+      'empty' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+    },
+    'circ' => {
+      'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+    }
   },
 
   # uncomment to use preloaded databases (useful when doing lots of