--- Operon.pm.org	2007-08-27 15:53:15.000000000 -0400
+++ Operon.pm	2007-08-27 15:57:19.000000000 -0400
@@ -100,25 +100,29 @@

 	my $flag = 0;
 	open(FILE, $dir) || die($!);
-	while(<FILE>){
+	while (<FILE>) {
 	    chomp;
-	    
-	    if(/^\(1\)/){
-		$flag ++;
-		next;
+
+	    if (/^Columns\:/) {
+	      $flag++;
+	      next;
+	    }
+	    elsif(/^\t\(\d\)\s/) {
+	      $flag++;
+	      next;
 	    }
-	    
-	    if($flag){
+
+	    if($flag == 5){

 		my %geneOrder;

 		my ($operon, $num, $direction, $genes) = split(/\t/, $_, 4);
 		next unless($num >= 2);
-		
+
 		foreach my $genepair (split(/,/, $genes)){
 		    my ($gene, $locustag) = split(/\|/, $genepair, 2);
-		    
 		    my $cds = $gb->gene2id($locustag);
+
 		    $cds = $gb->gene2id($gene) unless(length $cds);

 		    if($cds){
