add synonyms from the dead names column. NOTE still need to get the Mapper...

add synonyms from the dead names column. NOTE still need to get the Mapper routine to dump non primary xref synonyms

misc-scripts/xref_mapping/XrefParser/HUGOParser.pm

@@ -9,6 +9,7 @@ use vars qw(@ISA);
 @ISA = qw(XrefParser::BaseParser);
 my $xref_sth ;
 my $dep_sth;
+my $syn_sth;
 
 # --------------------------------------------------------------------------------
 # Parse command line and run if being run directly
@@ -42,6 +43,7 @@ sub run {
   my $dir = dirname($file);
 
   my %hugo;
+  my %syn;
 
   open (ENS4, $dir."/ens4.txt") || die "Can't open hugo ens4 $dir/ens4.txt\n";
   #HGNC    Symbol  Literature Aliases      Withdrawn Symbols
@@ -55,6 +57,9 @@ sub run {
     my $label = $array[1];
 
     $hugo{$hgnc} = $label;
+    if(defined($array[3])){
+      $syn{$hgnc}  = $array[3];
+    }
 
   }
   close ENS4;
@@ -83,6 +88,13 @@ sub run {
       else{
 	XrefParser::BaseParser->add_to_xrefs($master,$hgnc,'',$hugo{$hgnc},"","",$source_id,$species_id,$count);
 	$count++;
+	if(defined($syn{$hgnc})){ #dead name add to synonym
+	  my @array = split(',\s*',$syn{$hgnc});
+	  foreach my $arr (@array){
+#	    print "adding synonym ".$arr." for ".$hugo{$hgnc}." ($hgnc)\n";
+	    XrefParser::BaseParser->add_to_syn($hgnc, $source_id, $arr);
+	  }
+	}
       }
       #	print "$array[1]\tSPTR\t$hgnc\tHUGO\t$hugo_id{$hgnc}\t$hugo_syn{$hgnc}\tXREF\n";
     }