use DBI; 
my $dbh = DBI->new('DBI:mysql:database=kmers;host=127.0.0.1','mysql_user','');
my $query = "INSERT INTO matrix VALUES (?,?)";
my $sth = $dbh->prepare($query);

for ($n=0; $n<scalar @line; $n++){
#open each kmer file
	open(my $KMER, $line[$n]) or die "Can't open file \"$line[$n]\"\n\n";
	my @kmers = <$KMER>;
	my @all_kmer;
	my $kmer;
	foreach $kmer (@kmers){
		my @split = split(/\s+/,$kmer); #obtain kmer reference number
		# for now we don't have to populate the big %matrix, commented 
		# $matrix{$n}{split[0]} = 1;
		# $sum{$split[0]}++;
                $sth->execute($n,$split[0]);
	}
	close $KMER;
}
$sth->finish();