From 7f349719df1c464cc17c7c98c492eff0660182dc Mon Sep 17 00:00:00 2001
From: Alistair Rust <rust@sanger.ac.uk>
Date: Thu, 2 Jan 2003 16:23:03 +0000
Subject: [PATCH] A non-fussy update method to enable (primarily) the addition
of display_xref_ids calculated in the protein pipeline to genes that already
exist in the db.
As implemented the method can also update the type and analysis
fields. If any one of the display_xref_id, type or analysis fields
have changed on the gene being updated, all of these fields are
updated.
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 57 ++++++++++++++++++++++++
1 file changed, 57 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index a36f1a3ebc..7443fda691 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -1025,6 +1025,63 @@ sub get_display_xref_id {
+=head2 update
+
+ Arg [1] : Bio::EnsEMBL::Gene
+ Example : $gene_adaptor->update($gene);
+ Description: Updates a gene in the database
+ Returntype : None
+ Exceptions : thrown if the $gene is not a Bio::EnsEMBL::Gene
+ warn if trying to update the number of attached transcripts. This
+ is a far more complex process and is not yet implemented.
+ warn if the method is called on a gene that does not exist in the
+ database.
+ Caller : general
+
+=cut
+
+sub update {
+ my ($self,$gene) = @_;
+ my $update = 0;
+
+ if( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
+ $self->throw("Must update a gene object, not a $gene");
+ }
+
+ my $sth = $self->prepare("SELECT type, analysis_id, transcript_count, display_xref_id
+ FROM gene
+ WHERE gene_id = ?
+ ");
+
+ $sth->execute($gene->dbID);
+
+ if ( my ($type, $analysis, $transcripts, $dxref_id) = $sth->fetchrow_array() ){
+
+ if ( $dxref_id != $gene->display_xref ) { $update = 1; }
+ elsif ( $type ne $gene->type ) { $update = 1; }
+ elsif ( $analysis != $gene->analysis->dbID ) { $update = 1; }
+ elsif ( $transcripts != scalar(@{$gene->get_all_Transcripts})) {
+ $self->warn("Trying to update the number of transcripts on a stored gene. Not yet implemented.");
+ }
+
+ if ( $update ) {
+
+ $sth = $self->prepare("UPDATE gene
+ SET type = '$type',
+ analysis_id = $analysis,
+ display_xref_id = $dxref_id
+ WHERE gene_id = ?
+ ");
+
+ $sth->execute($gene->dbID);
+ }
+ }
+ else {
+ $self->warn("Trying to update a gene that is not in the database. Try store\'ing first.");
+ }
+}
+
+
1;
__END__
--
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