From 9011d3bb2e944a0aed1b83aa4c579842983d6c7c Mon Sep 17 00:00:00 2001
From: Simon Brent <sb23@sanger.ac.uk>
Date: Thu, 27 Sep 2012 09:52:09 +0000
Subject: [PATCH] merging changes from branch-ensembl-68
---
modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm | 5 ++---
modules/t/MultiTestDB.conf.example | 11 ++++++++---
2 files changed, 10 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm b/modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm
index 43114be8b3..aa69c265f1 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm
+++ b/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()};
diff --git a/modules/t/MultiTestDB.conf.example b/modules/t/MultiTestDB.conf.example
index 9002f09fba..84d8477077 100644
--- a/modules/t/MultiTestDB.conf.example
+++ b/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
--
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