sub iterblast{

	# settings
	my $myblast    = "blastall -p blastn -m 8";
	my $starterseq = "/share/home/tjuh/Thema12-2011/Project/testblast/matchedhits.fasta";
	my $blastdb    = "/share/home/tjuh/Thema12-2011/Project/databases/termite_hindgut/hindgut_db";
	my $outputroot = "/share/home/tjuh/Thema12-2011/Project/testblast/test1";
	my $evalue     = 0.01;
	my $wordsize   = 11;
	my $roundlimit = 4;
	
	# output files:
	my $seq_db_fasta = $outputroot . ".tmp";
	my $seq_db_all   = $outputroot . ".all";
	my $logfile      = $outputroot . ".log";

	# remove existing files
	system("rm -rf $seq_db_fasta");
	system("rm -rf $seq_db_all");
	system("rm -rf $logfile");
	
	open(LOG,">$logfile");
	print LOG "Configurations:\n";
	print LOG "Input file       : $starterseq\n";
	print LOG "Output files     : $outputroot\-\n";
	print LOG "Blast Engine     : $myblast\n";
	print LOG "Target database  : $blastdb\n";
	print LOG "E-value cut-off  : $evalue\n";
	print LOG "Blast word size  : $wordsize\n";
	print LOG "Blast round limit: $roundlimit\n\n";
	print LOG "Runs:\n";
	
	# hits hash
	my %hits = ();
	my %queryids = ();
	
	# Start the iterative blastn rounds
	for (my $round = 1; $round <= $roundlimit; $round++) {

		my $hitcount = 0;
		my $infile = "";
		
		# the initial fasta file is only run once
		if ($round > 1) {
			$infile = $seq_db_fasta;
		} else {
			$infile = $starterseq;
		}
		
		my $saveblst = $outputroot . ".txt";
		system("rm -rf $saveblst");
		
		# print LOG info
		my $curtime = `date`; chomp($curtime);
		print LOG "$curtime - Blast seq: $infile\n";
		print LOG "$curtime - Blast db : $blastdb\n";
		
		# run blast
		system("$myblast -i $infile -d $blastdb -o $saveblst -e $evalue -W $wordsize");

		open(PARSE, "<$saveblst");
		open(FASTA, ">$seq_db_fasta");
		
			# parse blast output (tab form) and add matched id's in hits hash
			my @lines = ();

			while (my $line = <PARSE>){
				chomp $line;
				@lines = split(/\t/, $line);
				$queryids{$lines[0]}++;
				$hits{$lines[1]}++;
			}

			#print "Hash size queryids: ", scalar keys %queryids, "\n";			
			#print "Hash size hits: ", scalar keys %hits, "\n";
			
			# get header and sequence with 'fastacmd' and write to new fasta file
			while (my $key = each %hits){
				#print $key . "\n";
				if (exists($queryids{$key})){ # only writes uniq ids to file
					#print $key . "\n";
					$queryids{$key} = 1;
				} else {
					system("fastacmd -d $blastdb -s 'lcl|$key' >> $seq_db_fasta");
					$hitcount++;
				}
			}
		
			print LOG "Round $round has $hitcount unique hits\n\n";
			
			# evaluate if to run for next blast round
			if ($hitcount == 0) {
				print LOG "Hitcount: $hitcount through Round $round ==> STOP\n";
				$round = $roundlimit;
			}
		
		close(FASTA);			
		close(PARSE);
		
	}
	print "Total uniq hits found in all rounds: ", scalar keys %hits, "\n";

	close(LOG);
}