1 the only
2 significant
3 part
4 is 
5 a 
6 number
7 before 
8 the 
9 first 
10 space 
11 character

##</code><code>##

#!/usr/bin/perl
use strict;
use warnings;

my %matrix;
my %sum;

#inport file names
my $fn = $ARGV[0];
chomp $fn;
open (my $FILE, $fn) or die "Can't open file \"$fn\"\n\n";

chomp(my @line = <$FILE>);
my $n;

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]}++;
	}
	close $KMER;
}
close $FILE;

#creat outfile
my $outfile = $ARGV[1];
open (my $OUT, '>' .$outfile) or die "\nUnable to create $outfile\n";

#sum up
foreach my $k (keys %sum){
	print $OUT "$sum{$k}\n";
}

##</code><code>##

CREATE DATABASE kmers;
CREATE TABLE matrix (file int, number int, key (file), key (number)); 

##</code><code>##

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();


##</code><code>##


my $count_query = "SELECT number,COUNT(number) FROM matrix GROUP BY number ORDER BY number";
$sth = $dbh->prepare($count_query);

##</code><code>##

#sum up
#foreach my $k (keys %sum){
#	print $OUT "$sum{$k}\n";
#}

$sth->execute(); 
while (my $res = $sth->fetchrow_arrayref()) {
   print $OUT $res->[1]\n";
}