From a4f9f3009cbc6167713f80767a09fca8167aa76e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 4 Dec 2009 11:43:03 +0000
Subject: [PATCH] Patch to get_species_and_object_type(): If a database
adaptor does not have a corresponding 'species.stable_id_prefix' meta key it
should not be skipped completely. Solves a problem with Eugene's yeast
database.
---
modules/Bio/EnsEMBL/Registry.pm | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index e53d2e5ba7..41a84f7208 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -2428,8 +2428,13 @@ sub get_species_and_object_type {
my $species = $dba->species();
+ my $fetched_something = 0;
+
while ( $sth->fetch() ) {
+ $fetched_something = 1;
+
my $standard_prefix = 0;
+
foreach my $allowed_prefix (@allowed_prefixes) {
if (
substr( $prefix, 0, length($allowed_prefix) ) eq
@@ -2453,6 +2458,12 @@ sub get_species_and_object_type {
}
+ if ( !$fetched_something ) {
+ # This database didn't have a matching
+ # 'species.stable_id_prefix' key in its meta table.
+ push( @nonstandard_prefix_species, $species );
+ }
+
} ## end foreach my $dba ( @{ $self->get_all_DBAdaptors...})
} ## end if ( !%stable_id_prefix)
--
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