From 36fc2e6a7a35f762d81db344fa8cab05206c9a98 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 31 Mar 2009 11:57:52 +0000
Subject: [PATCH] new test code to calculate display xrefs using the xref
database and SQL only. So much, much faster as just simple sql instead of
gettin gall genes, then all transcripts then all dbentries. Caveat though is
that all the xrefs have to be in the xref database and cannot be used to an
update mode. i.e. just adding one particular source. Can only be used whan
adding ALL sources possible.
---
.../xref_mapping/XrefMapper/DisplayXrefs.pm | 130 +++++++++++++++++-
1 file changed, 128 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
index 7dcde17a37..6d7934c691 100644
--- a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
@@ -26,6 +26,7 @@ sub new {
$self->core($mapper->core);
$self->xref($mapper->xref);
$self->mapper($mapper);
+ $self->verbose($mapper->verbose);
return $self;
}
@@ -99,14 +100,14 @@ sub build_transcript_and_gene_display_xrefs {
my ($presedence, $ignore) = @{$self->transcript_display_xref_sources()};
my $i=0;
my %level;
-# print "precedense in reverse order:-\n";
+ print "precedense in reverse order:-\n" if($self->verbose);
foreach my $name (reverse (@$presedence)){
$i++;
if(!defined($external_name_to_id{$name})){
print STDERR "unknown external database name *$name* being used\n";
}
$level{$external_name_to_id{$name}} = $i;
-# print "\t".$name."\t$i\n";
+ print "\t".$name."\t$i\n" if($self->verbose);
}
$self->build_genes_to_transcripts();
@@ -819,4 +820,129 @@ sub build_meta_timestamp{
}
+
+sub pump_up_the_jam{
+ my $self = shift;
+
+my $sql =(<<SQL);
+ CREATE TABLE display_xref_prioritys(
+ source_id INT NOT NULL,
+ priority INT NOT NULL,
+ PRIMARY KEY (source_id)
+ ) COLLATE=latin1_swedish_ci TYPE=InnoDB
+SQL
+
+ my $sth = $self->xref->dbc->prepare($sql);
+ $sth->execute;
+ $sth->finish;
+
+ my ($presedence, $ignore) = @{$self->transcript_display_xref_sources()};
+ my $i=0;
+
+ my $ins_p_sth = $self->xref->dbc->prepare("INSERT into display_xref_prioritys (source_id, priority) values(?, ?)");
+ my $get_source_id_sth = $self->xref->dbc->prepare("select source_id from source where name like ?");
+
+#
+# So the higher the number the better then
+#
+
+
+ foreach my $name (reverse (@$presedence)){
+ $i++;
+ $get_source_id_sth->execute($name);
+ my $source_id;
+ $get_source_id_sth->bind_columns(\$source_id);
+ while($get_source_id_sth->fetch){
+ $ins_p_sth->execute($source_id, $i);
+ }
+ }
+ $ins_p_sth->finish;
+ $get_source_id_sth->finish;
+
+#my $display_xref_sql =(<<DXS);
+# SELECT (if(gtt1.gene_id,gtt1.gene_id,0)+if(gtt2.gene_id,gtt2.gene_id,0)+if(gtt3.gene_id,gtt3.gene_id,0)) as gene,(if(gtt1.transcript_id,gtt1.transcript_id,0)+if(gtt2.transcript_id,gtt2.transcript_id,0)+if(gtt3.transcript_id,gtt3.transcript_id,0)) , p.priority, x.xref_id, ox.ensembl_object_type, x.label
+# FROM (source s, xref x, identity_xref ix, display_xref_prioritys p, object_xref ox)
+# LEFT JOIN gene_transcript_translation gtt1 on (gtt1.gene_id = ox.ensembl_id and ox.ensembl_object_type = "Gene")
+# LEFT JOIN gene_transcript_translation gtt2 on (gtt2.transcript_id = ox.ensembl_id and ox.ensembl_object_type = "Transcript")
+# LEFT JOIN gene_transcript_translation gtt3 on (gtt3.translation_id = ox.ensembl_id and ox.ensembl_object_type = "Translation")
+# WHERE x.source_id = s.source_id
+# AND x.xref_id = ox.xref_id
+# AND ox.ox_status = "DUMP_OUT"
+# AND ox.object_xref_id = ix.object_xref_id
+# AND p.source_id = s.source_id
+# ORDER BY gene DESC, p.priority DESC, (ix.target_identity+ix.query_identity) DESC
+#DXS
+
+#######################################################################
+
+my $display_xref_sql =(<<DXS);
+ SELECT gtt.gene_id, gtt.transcript_id, p.priority, x.xref_id, ox.ensembl_object_type, x.label
+ FROM source s, xref x, object_xref ox, identity_xref ix, gene_transcript_translation gtt, display_xref_prioritys p
+ WHERE x.source_id = s.source_id
+ AND x.xref_id = ox.xref_id
+ AND ox.ox_status = "DUMP_OUT"
+ AND ( (ox.ensembl_object_type = "Transcript" and gtt.transcript_id = ox.ensembl_id)
+ OR (ox.ensembl_object_type = "Translation" and gtt.translation_id = ox.ensembl_id)
+ OR (ox.ensembl_object_type = "Gene" and gtt.gene_id = ox.ensembl_id)
+ )
+ AND ox.object_xref_id = ix.object_xref_id
+ AND p.source_id = s.source_id
+ ORDER BY gtt.gene_id DESC, p.priority DESC, (ix.target_identity+ix.query_identity) DESC
+DXS
+
+########################################################################
+
+ my %seen_transcript; # first time we see it is the best due to ordering :-)
+ # so either write data to database or store
+
+
+ my $gene_sth = $self->core->dbc->prepare("select x.display_label from gene g, xref x where g.display_xref_id = x.xref_id and g.gene_id = ?");
+ my $tran_sth = $self->core->dbc->prepare("select x.display_label from transcript t, xref x where t.display_xref_id = x.xref_id and t.transcript_id = ?");
+
+
+ my $last_gene = 0;
+
+ my $display_xref_sth = $self->xref->dbc->prepare($display_xref_sql);
+
+ $display_xref_sth->execute();
+ my ($gene_id, $transcript_id, $p, $xref_id, $type, $label); # remove labvel after testig it is not needed
+ $display_xref_sth->bind_columns(\$gene_id, \$transcript_id, \$p, \$xref_id, \$type, \$label);
+ while($display_xref_sth->fetch()){
+# print "$gene_id, $transcript_id, $p, $xref_id, $type, $label\n";
+# if(defined($label) && $label =~ /\D+/){ # not just a number
+ if($gene_id != $last_gene){
+ $self->check($gene_id,$label, $gene_sth, "Gene");
+ $last_gene = $gene_id;
+ }
+ if($type ne "Gene"){
+ if(!defined($seen_transcript{$transcript_id})){ # not seen yet so its the best
+ $self->check($transcript_id, $label, $tran_sth, "Transcript");
+ }
+ $seen_transcript{$transcript_id} = $xref_id;
+
+ }
+# }
+ }
+ $display_xref_sth->finish;
+}
+
+
+sub check{
+ my $self = shift;
+ my $id = shift;
+ my $label = shift;
+ my $sth = shift;
+ my $type = shift;
+
+ $sth->execute($id);
+ my $old_label;
+ $sth->bind_columns(\$old_label);
+ $sth->fetch;
+
+ if($old_label ne $label){
+ print "ERROR: $type ($id) has different display_xrefs ??? old:$old_label new:$label\n";
+ }
+}
+
+
1;
--
GitLab