From 534a21371149cc2f76343196b0c7161033df3564 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 29 Oct 2007 15:54:11 +0000
Subject: [PATCH] added get_all_Genes_by_source and made get_all_Genes_by type
select at teh sql level rather than later on using grep
---
modules/Bio/EnsEMBL/Slice.pm | 54 ++++++++++++++++++++++++------------
1 file changed, 37 insertions(+), 17 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 02d70ce45b..92c082cf10 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -1870,6 +1870,10 @@ sub get_all_SNPs_transcripts {
than being lazy-loaded on request. This will result in a
significant speed up if the Transcripts and Exons are going to
be used (but a slow down if they are not).
+ Arg [4] : (optional) string $source
+ The source of the genes to retrieve.
+ Arg [5] : (optional) string $biotype
+ The biotype of the genes to retrieve.
Example : @genes = @{$slice->get_all_Genes};
Description: Retrieves all genes that overlap this slice.
Returntype : listref of Bio::EnsEMBL::Genes
@@ -1880,7 +1884,7 @@ sub get_all_SNPs_transcripts {
=cut
sub get_all_Genes{
- my ($self, $logic_name, $dbtype, $load_transcripts) = @_;
+ my ($self, $logic_name, $dbtype, $load_transcripts, $source, $biotype) = @_;
if(!$self->adaptor()) {
warning('Cannot get Genes without attached adaptor');
@@ -1904,7 +1908,7 @@ sub get_all_Genes{
$ga = $self->adaptor->db->get_GeneAdaptor();
}
- return $ga->fetch_all_by_Slice( $self, $logic_name, $load_transcripts);
+ return $ga->fetch_all_by_Slice( $self, $logic_name, $load_transcripts, $source, $biotype);
}
=head2 get_all_Genes_by_type
@@ -1941,13 +1945,39 @@ sub get_all_Genes_by_type{
return [];
}
- my @out = grep { $_->biotype eq $type }
- @{ $self->get_all_Genes($logic_name, undef, $load_transcripts)};
-
- return \@out;
+ return $self->get_all_Genes($logic_name, undef, $load_transcripts, undef, $type);
}
+=head2 get_all_Genes_by_source
+
+ Arg [1] : string source
+ Arg [2] : (optional) boolean $load_transcripts
+ If set to true, transcripts will be loaded immediately rather
+ than being lazy-loaded on request. This will result in a
+ significant speed up if the Transcripts and Exons are going to
+ be used (but a slow down if they are not).
+ Example : @genes = @{$slice->get_all_Genes_by_source('ensembl')};
+ Description: Retrieves genes that overlap this slice of source $source.
+
+ Returntype : listref of Bio::EnsEMBL::Genes
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub get_all_Genes_by_source {
+ my ($self, $source, $load_transcripts) = @_;
+
+ if(!$self->adaptor()) {
+ warning('Cannot get Genes without attached adaptor');
+ return [];
+ }
+
+ return $self->get_all_Genes(undef, undef, $load_transcripts, $source);
+}
+
=head2 get_all_Transcripts
Arg [1] : (optional) boolean $load_exons
@@ -2856,6 +2886,7 @@ sub get_generic_features {
}
+
#
# Bioperl Bio::PrimarySeqI methods:
#
@@ -2972,17 +3003,6 @@ sub get_all_supercontig_Slices {
}
-=head2 get_all_Genes_by_source
-
- Description: DEPRECATED use get_all_Genes instead
-
-=cut
-
-sub get_all_Genes_by_source {
- deprecate("Use get_all_Genes() instead");
- return get_all_Genes(@_);
-}
-
--
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