#Open data file;
chomp($paths[1]);
my ($sfile) = $paths[1].$ARGV[0];
open my $fain,'<', $sfile
    or die "Unable to open $sfile\nError: $!\n";

my $length = $paths[3];
my $line = 0;
my %count;
while (my $fasta = <$fain>){
    
    if ($fasta !~ m/^>/){
                while ($fasta =~ /(.{$length})/g) {
                $count{$1}++;
                }
    }
    
    if ($fasta =~ m/^>/){
        #Print ID line
            print "$_ $count{$_}\n" for sort keys %count;
            %count = ();
            $line++;
            chomp($fasta);
            print "$line|$fasta\n";
    }
}
print "$_ $count{$_}\n" for sort keys %count;