From d836fc703fdd7bd6de6a3f899518f85db26f7cb3 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Tue, 21 May 2013 16:41:26 +0000
Subject: [PATCH] [ENSCORESW-475] fixing the dbentry return to prioritise
genes, transcripts and translations found on reference slices
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 10 +++++-----
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 5 ++++-
modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm | 13 ++++++++++---
3 files changed, 19 insertions(+), 9 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 19e12072e6..2d390514b7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -837,12 +837,12 @@ sub fetch_all_by_external_name {
my @ids = $entryAdaptor->list_gene_ids_by_extids($external_name, $external_db_name, $override);
- my %genes_by_dbIDs =
- map { $_->dbID(), $_ } @{$self->fetch_all_by_dbID_list(\@ids)};
+ my %genes_by_dbIDs = map { $_->dbID(), $_ } @{$self->fetch_all_by_dbID_list(\@ids)};
- my @result = map { $genes_by_dbIDs{$_} } @ids;
-
- return \@result;
+ my @features = map { $genes_by_dbIDs{$_} } @ids;
+ my @reference = grep { $_->slice()->is_reference() } @features;
+ my @non_reference = grep { ! $_->slice()->is_reference() } @features;
+ return [ @reference, @non_reference ];
}
=head2 fetch_all_by_description
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 933d491abb..7c459cbfd5 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -519,7 +519,10 @@ sub fetch_all_by_external_name {
$entryAdaptor->list_transcript_ids_by_extids( $external_name,
$external_db_name, $override );
- return $self->fetch_all_by_dbID_list( \@ids );
+ my @features = @{ $self->fetch_all_by_dbID_list( \@ids ) };
+ my @reference = grep { $_->slice()->is_reference() } @features;
+ my @non_reference = grep { ! $_->slice()->is_reference() } @features;
+ return [ @reference, @non_reference ];
}
=head2 fetch_all_by_GOTerm
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index 0de5dfafab..9588fbd43d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -313,16 +313,23 @@ sub fetch_all_by_external_name {
my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
- my @out;
+ my @reference;
+ my @non_reference;
foreach my $id (@ids) {
my $transcript = $transcript_adaptor->fetch_by_translation_id($id);
if ( defined($transcript) ) {
- push @out, $self->fetch_by_Transcript($transcript);
+ my $translation = $self->fetch_by_Transcript($transcript);
+ if($transcript->slice()->is_reference()) {
+ push(@reference, $translation);
+ }
+ else {
+ push(@non_reference, $translation);
+ }
}
}
- return \@out;
+ return [@reference, @non_reference];
}
=head2 fetch_all_by_GOTerm
--
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