#!/usr/local/bin/perl -w 
$| = 1;
#generate promoters
my $Bases = "ACGT";
#my @PromoterLenghts = ($PromoterMinLenght...$PromoterMaxLength);
my @PromoterLenghts = (4);
my $PromotroListLength = $#PromoterLenghts;
$PromotroListLength ++;
#unlink 'permute.txt';
my ($currLenght, $permutelist_filename);
foreach $currLenght (@PromoterLenghts){
	$permutelist_filename = &permute_bases ($currLenght, $Bases);	
}
#print "Sequences file $permutelist_filename\n";

open (PIN, "permute.txt")||die "Can't open  file: $!\n";
open (OUTPUT, ">output.txt")||die "Can't open  file: $!\n";
while (<PIN>){
	$promoter = $_;
	chomp $promoter;
	#do intrestering stuff with promoter sequence
	print OUTPUT "$promoter\n";
}
close PIN ||die "Could not close sequences file: $!";
close OUTPUT ||die "Could not close output file: $!";
unlink 'permute.txt';	

#####################################################################
sub permute_bases {
	my( $length, $bases )= @_;
	my @bases= split //, $bases;
	my @digit= (0) x $length;
	my $seq= $bases[0] x $length;
	my $permutelist_filename = "permute.txt";
	open  (PERMUTEOUT, ">>$permutelist_filename");   
	while(  1  ) {
		print PERMUTEOUT $seq,$/;
		print $seq,$/;
		my $pos= 0;
		while(  @bases <= ++$digit[$pos]  ) {
			substr( $seq, $pos, 1 )= $bases[ $digit[$pos]= 0 ];
		return if $length <= ++$pos;
		}
		substr( $seq, $pos, 1 )= $bases[ $digit[$pos] ];
	}
    close PERMUTEOUT||die"Could not close $permutelist_filename: $!";
	return ($permutelist_filename);
}