Operon documentation.

sub set_operon {
    my @args = opt_get(@_);
    my $gb = shift @args;

    if ($gb->{LOCUS}->{id} eq 'U00096' || $gb->{LOCUS}->{id} eq 'NC_000913'){

	my $url = "http://regulondb.ccg.unam.mx:80/data/OperonSet.txt";
	my $dir = $ENV{HOME} . '/.glang/data/OperonSet.txt';
	mirror($url, $dir);
	die("setOperon: cannot retrieve data from RegulonDB.") unless(-e $dir);

	my $flag = 0;
	open(FILE, $dir) || die($!);
	while(<FILE>){
	    chomp;
	    
	    if(/^\(1\)/){
		$flag ++;
		next;
	    }
	    
	    if($flag){

		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){
			$gb->{$cds}->{operon} = $operon;
			$geneOrder{$cds} = $gb->{$cds}->{start};
		    }
		}

		my $i = 1;
		if($direction eq 'forward'){
		    foreach my $cds (sort {$geneOrder{$a} <=> $geneOrder{$b}} keys %geneOrder){
			$gb->{$cds}->{operonN} = $i;
			$i ++;
		    }
		}else{
		    foreach my $cds (sort {$geneOrder{$b} <=> $geneOrder{$a}} keys %geneOrder){
			$gb->{$cds}->{operonN} = $i;
			$i ++;
		    }
		}

	    }else{
		msg_error($_, "\n");
	    }
	}
	close(FILE);

	foreach my $cds ($gb->cds()){
	    $gb->{$cds}->{operonN} = 0 unless(length $gb->{$cds}->{operon});
	}

   }else{
       msg_error("No Operon data for this species.\n\n");
   }

    return 1;
}