From 2901a1ad82341adc41a76e54c1cc6dd74578531b Mon Sep 17 00:00:00 2001
From: Jan-hinnerk Vogel <jhv@sanger.ac.uk>
Date: Wed, 2 Aug 2006 15:12:42 +0000
Subject: [PATCH] fetch_all_by_biotype added
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 30 ++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 93a7fc6102..ad8f1b4b48 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -205,6 +205,36 @@ sub fetch_by_stable_id {
return $gene;
}
+
+
+=head2 fetch_all_by_biotype
+
+ Arg [1] : String $biotype
+ The biotype of the gene to retrieve
+ Example : $gene = $gene_adaptor->fetch_all_by_biotype('protein_coding') ;
+ Description: Retrieves an array reference of gene objects from the database via its biotype.
+ The genes will be retrieved in its native coordinate system (i.e.
+ in the coordinate system it is stored in the database). It may
+ be converted to a different coordinate system through a call to
+ transform() or transfer(). If the gene or exon is not found
+ undef is returned instead.
+ Returntype : listref of Bio::EnsEMBL::Gene
+ Exceptions : if we cant get the gene in given coord system
+ Caller : general
+ Status : At Risk
+
+=cut
+
+sub fetch_all_by_biotype {
+ my ($self, $biotype) = @_;
+
+ my $constraint = "g.biotype = '$biotype' and g.is_current = 1" ;
+ my @genes = @{ $self->generic_fetch($constraint) };
+ return \@genes ;
+}
+
+
+
=head2 fetch_all_versions_by_stable_id
Arg [1] : String $stable_id
--
GitLab