From d09ce225461d237537248e872791f571e92dc2c0 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 23 May 2013 12:24:12 +0000
Subject: [PATCH] [ENSCORESW-479]. Making this module better at handling
homologue Compara errors and also get it to die when you try to get
homologues without a compara adaptor configured
---
modules/Bio/EnsEMBL/Gene.pm | 59 +++++++++++++++++++++++--------------
modules/t/gene.t | 14 ++++-----
2 files changed, 43 insertions(+), 30 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index cb87ed6394..9269744af0 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -818,12 +818,17 @@ sub get_all_Exons {
=head2 get_all_homologous_Genes
+ Arg[1] : String The compara synonym to use when looking for a database in the
+ registry. If not provided we will use the very first compara database
+ we find.
Description: Queries the Ensembl Compara database and retrieves all
Genes from other species that are orthologous.
REQUIRES properly setup Registry conf file. Meaning that
one of the aliases for each core db has to be "Genus species"
e.g. "Homo sapiens" (as in the name column in genome_db table
in the compara database).
+
+ The data is cached in this Object for faster re-retreival.
Returntype : listref [
Bio::EnsEMBL::Gene,
Bio::EnsEMBL::Compara::Homology,
@@ -836,37 +841,32 @@ sub get_all_Exons {
=cut
sub get_all_homologous_Genes {
- my $self = shift;
-
- if( exists( $self->{'homologues'} ) ){
- return $self->{'homologues'};
- }
- $self->{'homologues'} = [];
-
- # TODO: Find a robust way of retrieving compara dba directly.
- # For now look through all DBAs
- my $compara_dba;
- foreach my $dba( @{Bio::EnsEMBL::Registry->get_all_DBAdaptors} ){
- if( $dba->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor') ){
- $compara_dba = $dba;
- last;
- }
+ my ($self, $db_synonym) = @_;
+
+ #Look for DBAdaptors which have a group of compara; these are compara DBAs.
+ #If given a synonym
+ my %args = (-GROUP => 'compara');
+ $args{-SPECIES} = $db_synonym if $db_synonym;
+ my ($compara_dba) = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors(%args)};
+ unless( $compara_dba ) {
+ throw("No compara found in Bio::EnsEMBL::Registry. Please fully populate the Registry or construct a Bio::EnsEMBL::Compara::DBSQL::DBAdaptor");
}
- unless( $compara_dba ){
- warning("No compara in Bio::EnsEMBL::Registry");
- return $self->{'homologues'};
+ my $compara_species = $compara_dba->species();
+ if( exists( $self->{'homologues'}->{$compara_species} ) ){
+ return $self->{'homologues'}->{$compara_species};
}
+ $self->{'homologues'}->{$compara_species} = [];
# Get the compara 'member' corresponding to self
my $member_adaptor = $compara_dba->get_adaptor('GeneMember');
my $query_member = $member_adaptor->fetch_by_source_stable_id
("ENSEMBLGENE",$self->stable_id);
- unless( $query_member ){ return $self->{'homologues'} };
+ unless( $query_member ){ return $self->{'homologues'}->{$compara_species} };
# Get the compara 'homologies' corresponding to 'member'
my $homology_adaptor = $compara_dba->get_adaptor('Homology');
my @homolos = @{$homology_adaptor->fetch_all_by_Member($query_member)};
- unless( scalar(@homolos) ){ return $self->{'homologues'} };
+ unless( scalar(@homolos) ){ return $self->{'homologues'}->{$compara_species} };
# Get the ensembl 'genes' corresponding to 'homologies'
foreach my $homolo( @homolos ){
@@ -882,10 +882,25 @@ sub get_all_homologous_Genes {
-description=>$member->description, );
}
my $hspecies = $member->genome_db->name;
- push @{$self->{'homologues'}}, [$hgene,$homolo,$hspecies];
+ push @{$self->{'homologues'}->{$compara_species}}, [$hgene,$homolo,$hspecies];
}
}
- return $self->{'homologues'};
+ return $self->{'homologues'}->{$compara_species};
+}
+
+=head2 _clear_homologues
+
+ Description: Removes any cached homologues from the Gene which could have been
+ fetched from the C<get_all_homologous_Genes()> call.
+ Returntype : none
+ Exceptions : none
+ Caller : general
+
+=cut
+
+sub _clear_homologues {
+ my ($self) = @_;
+ delete $self->{homologues};
}
diff --git a/modules/t/gene.t b/modules/t/gene.t
index a70031446b..7bd1ed0da7 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -2,6 +2,7 @@ use strict;
use warnings;
use Test::More;
+use Test::Exception;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Test::MultiTestDB;
@@ -80,14 +81,6 @@ debug("Links: " . scalar(@$links));
ok(scalar @$links == 6);
-SKIP: {
- my $compara_dba = Bio::EnsEMBL::Registry->get_DBAdaptor('multi', 'compara', 1);
- skip 'No comapra database adaptor found', 1 if !$compara_dba;
- my $homologies = $gene->get_all_homologous_Genes();
- debug("Homologies: " . scalar(@$homologies));
-
- ok(scalar @$homologies ? ($homologies->[0][0]->isa("Bio::EnsEMBL::Gene")) : 1);
-}
# now create a new gene ...
my $sa = $db->get_SliceAdaptor();
@@ -818,4 +811,9 @@ my $registry = 'Bio::EnsEMBL::Registry';
my ($species, $object_type, $db_type) = $registry->get_species_and_object_type('ENSG00000355555');
ok($species eq 'homo_sapiens' && $object_type eq 'Gene');
+# Testing compara dba retrieval
+{
+ dies_ok { $new_gene->get_all_homologous_Genes(); } 'No Compara DBAdaptor has been configured. No way to retrieve data';
+}
+
done_testing();
--
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