Oh! Thanks. Yes it is Estonian :D. Somehow I posted even a more erroneus code that I have here working - (Probably trying to make it neat or remove some stuff - glad I did not remove the comments as it made it possible to use your lingusitics skill :D)

#!/usr/bin/perl -w
use strict;
use warnings;
use Data::Dumper;
#kaks üheveerulist faili, prindib need veerud mis ühes on aga teises p
+ole
#ehk siis suurem fail miinus väiksem
my $num_args = $#ARGV + 1;
if ($num_args != 3) {
  print "\nUsage: ./lahutaja suurem väiksem vahe(output)\n";
  exit;
}
my $fasta=$ARGV[0];
my $quala=$ARGV[1];
my $out=$ARGV[2];
open  FA, "< $fasta"or die "Can't open $fasta: $!";
open  QA, "< $quala" or die "Can't open $quala: $!";
open  OUT,"> $out" or die "Can't open $out: $!";
     


my @bl = <QA>;
my @a = <FA>;
my %h;

@h{@bl} = @bl;
my @output=[grep {!exists $h{$_}} @a];

print Dumper @output ;
print OUT  @output;



close FA;
close QA;
close OUT;
[download]

was the original half-working piece