From 5e81d29f7d955f96ee5165b4bd50c72fd30e4524 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 1 Jun 2009 10:42:27 +0000
Subject: [PATCH] Add fetch_all_by_GOTerm_accession().
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 44 +++++++++++++++++++
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 44 +++++++++++++++++++
.../Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm | 44 +++++++++++++++++++
3 files changed, 132 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 926f10ce3d..93aab8b8f2 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -819,6 +819,50 @@ sub fetch_all_by_GOTerm {
return \@result;
}
+=head2 fetch_all_by_GOTerm_accession
+
+ Arg [1] : String
+ The GO term accession for which genes should be
+ fetched.
+
+ Example :
+
+ @genes =
+ @{ $gene_adaptor->fetch_all_by_GOTerm_accession(
+ 'GO:0030326') };
+
+ Description : Retrieves a list of genes that are associated with
+ the given GO term, or with any of its descendent
+ GO terms. The genes returned are in their native
+ coordinate system, i.e. in the coordinate system
+ in which they are stored in the database. If
+ another coordinate system is required then the
+ Gene::transfer or Gene::transform method can be
+ used.
+
+ Return type : listref of Bio::EnsEMBL::Gene
+ Exceptions : Throws of argument is not a GO term accession
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub fetch_all_by_GOTerm_accession {
+ my ( $self, $accession ) = @_;
+
+ if ( $accession !~ /^GO:/ ) {
+ throw('Argument is not a GO term accession');
+ }
+
+ my $goAdaptor =
+ Bio::EnsEMBL::Registry->get_adaptor( 'Multi', 'Ontology',
+ 'GOTerm' );
+
+ my $term = $goAdaptor->fetch_by_accession($accession);
+
+ return $self->fetch_all_by_GOTerm($term);
+}
+
=head2 fetch_all_alt_alleles
Arg [1] : Bio::EnsEMBL::Gene $gene
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 6d7057e25c..3b15999b28 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -514,6 +514,50 @@ sub fetch_all_by_GOTerm {
return \@result;
}
+=head2 fetch_all_by_GOTerm_accession
+
+ Arg [1] : String
+ The GO term accession for which genes should be
+ fetched.
+
+ Example :
+
+ @genes =
+ @{ $gene_adaptor->fetch_all_by_GOTerm_accession(
+ 'GO:0030326') };
+
+ Description : Retrieves a list of genes that are associated with
+ the given GO term, or with any of its descendent
+ GO terms. The genes returned are in their native
+ coordinate system, i.e. in the coordinate system
+ in which they are stored in the database. If
+ another coordinate system is required then the
+ Gene::transfer or Gene::transform method can be
+ used.
+
+ Return type : listref of Bio::EnsEMBL::Gene
+ Exceptions : Throws of argument is not a GO term accession
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub fetch_all_by_GOTerm_accession {
+ my ( $self, $accession ) = @_;
+
+ if ( $accession !~ /^GO:/ ) {
+ throw('Argument is not a GO term accession');
+ }
+
+ my $goAdaptor =
+ Bio::EnsEMBL::Registry->get_adaptor( 'Multi', 'Ontology',
+ 'GOTerm' );
+
+ my $term = $goAdaptor->fetch_by_accession($accession);
+
+ return $self->fetch_all_by_GOTerm($term);
+}
+
=head2 fetch_by_display_label
Arg [1] : String $label - display label of transcript to fetch
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index 2e6293a3d1..676273b160 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -270,6 +270,50 @@ sub fetch_all_by_GOTerm {
return \@result;
} ## end sub fetch_all_by_GOTerm
+=head2 fetch_all_by_GOTerm_accession
+
+ Arg [1] : String
+ The GO term accession for which genes should be
+ fetched.
+
+ Example :
+
+ @genes =
+ @{ $gene_adaptor->fetch_all_by_GOTerm_accession(
+ 'GO:0030326') };
+
+ Description : Retrieves a list of genes that are associated with
+ the given GO term, or with any of its descendent
+ GO terms. The genes returned are in their native
+ coordinate system, i.e. in the coordinate system
+ in which they are stored in the database. If
+ another coordinate system is required then the
+ Gene::transfer or Gene::transform method can be
+ used.
+
+ Return type : listref of Bio::EnsEMBL::Gene
+ Exceptions : Throws of argument is not a GO term accession
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub fetch_all_by_GOTerm_accession {
+ my ( $self, $accession ) = @_;
+
+ if ( $accession !~ /^GO:/ ) {
+ throw('Argument is not a GO term accession');
+ }
+
+ my $goAdaptor =
+ Bio::EnsEMBL::Registry->get_adaptor( 'Multi', 'Ontology',
+ 'GOTerm' );
+
+ my $term = $goAdaptor->fetch_by_accession($accession);
+
+ return $self->fetch_all_by_GOTerm($term);
+}
+
=head2 store
Arg [1] : Bio::EnsEMBL::Translation $translation
--
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