From ba096cfcd9dfce3775264634dadff9cab371e381 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 14 Apr 2005 10:33:03 +0000
Subject: [PATCH] added routine to add synonyms given accesion and source id
---
.../xref_mapping/XrefParser/BaseParser.pm | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index f9f9add7d1..deca2aabcd 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -15,6 +15,7 @@ my $add_xref_sth = undef;
my $add_direct_xref_sth = undef;
my $add_dependent_xref_sth = undef;
my $get_xref_sth = undef;
+my $add_synonym_sth = undef;
my $dbi;
my %dependent_sources;
@@ -826,6 +827,21 @@ sub add_to_xrefs{
}
+sub add_to_syn{
+ my ($self, $acc, $source_id, $syn) = @_;
+
+ if(!defined($add_synonym_sth)){
+ $add_synonym_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?)");
+ }
+ my $xref_id = get_xref($acc, $source_id);
+ if(defined($xref_id)){
+ $add_synonym_sth->execute($xref_id, $syn) || die "$dbi->errstr \n $xref_id\n $syn\n";
+ }
+ else{
+ die "Could not find acc $acc in xref table source = $source_id\n";
+ }
+}
+
# --------------------------------------------------------------------------------
# Add a single record to the direct_xref table.
# Note that an xref must already have been added to the xref table (xref_id passed as 1st arg)
--
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