added routine to add synonyms given accesion and source id

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)