From 5b6ab05543006a66ab29f53172b26d421da0930c Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 2 Nov 2012 15:26:35 +0000
Subject: [PATCH] removed LRG section as it is not currently used
---
.../xref_mapping/XrefMapper/OfficialNaming.pm | 90 -------------------
1 file changed, 90 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm b/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
index 9ceaff4d10..17d9dc2f7b 100644
--- a/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
@@ -240,13 +240,6 @@ SQ0
$official_name_used{$gene_symbol_xref_id} = 1;
}
- ############################################
- # If not found see if there is an LRG entry
- ############################################
- if(!defined($gene_symbol)){ # look for LRG
- ($gene_symbol, $gene_symbol_xref_id) = $self->find_lrg_hgnc($gene_id);
- }
-
####################################################
# If not found look for other valid database sources
# These are RFAM and miRBase, as well as Uniprot_genename
@@ -1171,89 +1164,6 @@ sub get_xref_id_for_gene_symbol{
}
return $xref_id;
}
-########################## START LRG BIT ######################################################
-
-sub get_lrg_find_sth{
- my $self = shift;
-
- if(!defined($self->{'_lrg_find_sth'})){
- my $sql=(<<'SQ2');
-SELECT x.label, x.xref_id, ox.object_xref_id, s.priority
- FROM xref x, object_xref ox, source s
- WHERE x.xref_id = ox.xref_id AND
- x.source_id = s.source_id AND
- s.name = ? AND
- ox.ensembl_id = ? AND
- ox.ensembl_object_type = ?
-SQ2
- $self->{'_lrg_find_sth'} =$self->xref->dbc->prepare($sql);
- }
- return $self->{'_lrg_find_sth'};
-}
-
-
-sub get_lrg_set_status_sth{
- my $self = shift;
-
- if(!defined($self->{'_lrg_set_status_sth'})){
- $self->{'_lrg_set_status_sth'} =
- $self->xref->dbc->prepare("update object_xref set ox_status = 'NO_DISPLAY' where object_xref_id = ?");
- }
- return $self->{'_lrg_set_status_sth'};
-}
-
-sub get_lrg_to_hgnc_sth{
- my $self = shift;
-
- if(!defined($self->{'_lrg_to_hgnc_sth'})){
- my $sql=(<<'SQ4');
-SELECT x.xref_id, s.priority
- FROM xref x,source s, object_xref ox
- WHERE x.xref_id = ox.xref_id AND
- x.source_id = s.source_id AND
- x.label = ? AND
- s.name = ? AND
- ox.ox_status = 'DUMP_OUT'
- ORDER BY s.priority
-SQ4
- $self->{'_lrg_to_hgnc_sth'} = $self->xref->dbc->prepare($sql);
- }
- return $self->{'_lrg_to_hgnc_sth'};
-}
-
-
-sub find_lrg_hgnc{
- my ($self, $gene_id) =@_;
- my $gene_symbol;
- my $gene_symbol_xref_id;
-
- my $lrg_find_sth = $self->get_lrg_find_sth();
- my $lrg_set_status_sth = $self->get_lrg_set_status_sth();
- my $lrg_to_hgnc_sth = $self->get_lrg_to_hgnc_sth();
-
- # look for LRG_HGNC_notransfer, if found then find HGNC equiv and set to this
- # print "LRG FOUND with no HGNC, should have gotten this via the alt allele table?? gene_id = $gene_id\n";
- $lrg_find_sth->execute("LRG_HGNC_notransfer", $gene_id, "Gene");
- my ($display, $xref_id, $object_xref_id, $level);
- $lrg_find_sth->bind_columns(\$display, \$xref_id, \$object_xref_id, \$level);
- while($lrg_find_sth->fetch){
- $lrg_set_status_sth->execute($object_xref_id); # set oc_status to no _display as we do not want this transferred,
- # just the equivalent hgnc
- my $new_xref_id = undef;
- my $pp;
- $lrg_to_hgnc_sth->execute($display,"HGNC");
- $lrg_to_hgnc_sth->bind_columns(\$new_xref_id,\$pp);
- $lrg_to_hgnc_sth->fetch;
- if(defined($new_xref_id)){
- $gene_symbol = $display;
- $gene_symbol_xref_id = $new_xref_id;
- }
- }
- return ($gene_symbol, $gene_symbol_xref_id);
-}
-
-#############################END LRG BIT ################################################
-
#
--
GitLab