#!/usr/bin/perl

use strict;
use warnings;

use Data::Dumper;
my ($file) = glob '*.fastq';

open $fh, $file;

my $analysis = []; # each element a sequence position
		   # at which we will put a hash of freqs
print localtime() . "\n";
while ( my $hdr = <$fh>) {
    my $seq = <$fh>;
    chomp $seq;
    analyse($seq, $analysis);
    $seq = <$fh> for (0 .. 1); # discard trailer
}
print localtime() . "\n";
print Dumper($analysis);

sub analyse {
    my ($seq, $analysis) = @_;
    my $pos = length($seq);
    while ($pos) {
	$analysis->[--$pos]{chop $seq}++;
    }
}