From 416140567c9cf8a0669627a67404645dcc3ebe23 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Fri, 16 Mar 2012 12:00:39 +0000
Subject: [PATCH] added method fetch_all_by_display_label and changed
fetch_by_display_label to return a gene on the reference slice if there is
one
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 44 ++++++++++++++++++++++--
1 file changed, 41 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 81301457e2..c82faefe78 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -182,8 +182,9 @@ sub list_seq_region_ids {
Arg [1] : String $label - display label of gene to fetch
Example : my $gene = $geneAdaptor->fetch_by_display_label("BRCA2");
Description: Returns the gene which has the given display label or undef if
- there is none. If there are more than 1, only the first is
- reported.
+ there is none. If there are more than 1, the gene on the
+ reference slice is reported or if none are on the reference,
+ the first one is reported.
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
@@ -197,12 +198,49 @@ sub fetch_by_display_label {
my $constraint = "x.display_label = ? AND g.is_current = 1";
$self->bind_param_generic_fetch($label,SQL_VARCHAR);
- my ($gene) = @{ $self->generic_fetch($constraint) };
+ my @genes = @{ $self->generic_fetch($constraint) };
+ my $gene;
+ if (scalar(@genes) > 1) {
+ foreach my $gene_tmp (@genes) {
+ if ($gene_tmp->slice->is_reference) {
+ $gene = $gene_tmp;
+ }
+ last if ($gene);
+ }
+ if (!$gene) {
+ $gene = @genes[0];
+ }
+
+ } elsif (scalar(@genes) == 1) {
+ $gene = @genes[0];
+ }
return $gene;
}
+=head2 fetch_all_by_display_label
+
+ Arg [1] : String $label - display label of genes to fetch
+ Example : my @genes = @{$geneAdaptor->fetch_by_display_label("PPP1R2P1")};
+ Description: Returns all genes which have the given display label or undef if
+ there are none.
+ Returntype : listref of Bio::EnsEMBL::Gene objects
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub fetch_all_by_display_label {
+ my $self = shift;
+ my $label = shift;
+
+ my $constraint = "x.display_label = ? AND g.is_current = 1";
+ $self->bind_param_generic_fetch($label,SQL_VARCHAR);
+ my $genes = $self->generic_fetch($constraint) ;
+ return $genes;
+}
=head2 fetch_by_stable_id
--
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