From af947b107a6edb289a4d1b3d19fead92f47a4f6d Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Thu, 5 Dec 2013 16:41:48 +0000
Subject: [PATCH] [ENSCORESW-777]. Added GeneAdaptor support for fetching genes
by source(s).
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 49 ++++++++++++++++++++++++
1 file changed, 49 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 50bd2444be..db37ea2bb3 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -251,6 +251,55 @@ sub fetch_by_stable_id {
return $gene;
}
+=head2 fetch_all_by_source
+
+ Arg [1] : String $source
+ listref of $sources
+ The source of the gene to retrieve. You can have as an argument a reference
+ to a list of sources
+ Example : $genes = $gene_adaptor->fetch_all_by_source('havana');
+ $genes = $gene_adaptor->fetch_all_by_source(['ensembl', 'vega']);
+ Description: Retrieves an array reference of gene objects from the database via its source or sources.
+ The gene will be retrieved in its native coordinate system (i.e.
+ in the coordinate system it is stored in the database). It may
+ be converted to a different coordinate system through a call to
+ transform() or transfer(). If the gene or exon is not found
+ undef is returned instead.
+ Returntype : listref of Bio::EnsEMBL::Gene
+ Exceptions : if we cant get the gene in given coord system
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub fetch_all_by_source {
+ my ($self, $source) = @_;
+ my @genes = @{$self->generic_fetch($self->source_constraint($source))};
+ return \@genes;
+}
+
+=head2 source_constraint
+
+ Arg [1] : String $source
+ listref of $sources
+ The source of the gene to retrieve. You can have as an argument a reference
+ to a list of sources
+ Description: Used internally to generate a SQL constraint to restrict a transcript query by source
+ Returntype : String
+ Exceptions : If source is not supplied
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub source_constraint {
+ my ($self, $sources, $inline_variables) = @_;
+ my $constraint = "g.is_current = 1";
+ my $in_statement = $self->generate_in_constraint($sources, 'g.source', SQL_VARCHAR, $inline_variables);
+ $constraint .= " and $in_statement";
+ return $constraint;
+}
+
=head2 fetch_all_by_biotype
Arg [1] : String $biotype
--
GitLab