# includes
use strict;
use Bio::ClusterIO;

# locals
my $dir	= $ARGV[0];
my %data;

# directory handling
if (-d !$dir) {
	print	"Directory does not exist!\n",
		"Program Terminating....\n";
	exit();
	}
opendir(DIR, $dir) || die "$dir: $!\n";
chdir($dir);
$dir =~ s/\\$//;

while (my $infile = readdir(DIR)) {

	if ((-T $infile) && ($infile =~ /^ds_ch(.{1,2})\.xml$/i)) {

		my %data;
		my $chromosome = $1;

		print "Processing $chromosome\n";

		my $parser = Bio::ClusterIO->new(
						-file	=>	$infile,
						-format	=>	'dbSNP'
						);

		while (my $record = $parser->next_cluster()) {

			if (my $class = $record->functional_class) {
				$class =~ s/^\s+//;
				$class =~ s/\s+$//;
				$data{$class}{$record->observed()}++;
				}
			}

		open(OUT, '>>', 'Results.txt');

		foreach my $class (keys(%data)) {
			foreach my $snp (keys(%{$data{$class}})) {
				print OUT "$chromosome\t$class\t$snp\t$data{$class}{$snp}\n";
				}
			}

		close(OUT);
		}

	}