Here's how I might have written that script, with the following changes to your version:

Please have a look, and if you have any questions, please let us know.

#!/usr/bin/env perl
use warnings;
use strict;
use Data::Dumper;
$Data::Dumper::Useqq = 1;
$Data::Dumper::Quotekeys = 0;
$Data::Dumper::Sortkeys = 1;

for my $folder ( grep {-d} glob('UNITAS_*') ) {
    print Data::Dumper->Dump([$folder], [qw/folder/]);
    opendir my $dh, $folder or die "$folder: $!";
    while ( my $file = readdir($dh) ) {
        next if $file !~ /\.mapped_sequences$/;
        print Data::Dumper->Dump([$file], [qw/file/]);
        
        my $reads = 0;
        open my $fileone, '<', "$folder/$file"
            or die "$folder/$file: $!";
        while ( my $tocount = <$fileone> ) {
            chomp $tocount;
            $tocount =~ s/>//g;
            next if $tocount =~ /[A-Za-z]/;
            if ( $tocount =~ /[0-9]/ ) {
                print Data::Dumper->Dump([$tocount], [qw/tocount/]);
                $reads += $tocount;
            }
        }
        close $fileone;
        print Data::Dumper->Dump([$reads], [qw/reads/]);
        
        my %hash;
        my $trftable = 'unitas.tRF-table.txt';
        open my $trf, '<', "$folder/$trftable"
            or die "$folder/$trftable: $!";
        <$trf> for 1 .. 4;
        while ( my $line = <$trf> ) {
            chomp $line;
            my @line = split /\t/, $line;
            #print Data::Dumper->Dump([\@line], [qw/*line/]);
            my $tRNAname;
            if ( $line[0] =~ s/tRNA-[^-]+-...// )
                { $tRNAname = $& }
            else
                { ( $tRNAname = $line[0] ) =~ s/-ENS.+$// }
            print Data::Dumper->Dump([$tRNAname], [qw/tRNAname/]);
            my $h = ( $hash{$tRNAname} //= {} );
            $h->{"5p-tR-halves"} += $line[ 1] / $reads * 1000000;
            $h->{"5p-tRFs"}      += $line[ 3] / $reads * 1000000;
            $h->{"3p-tR-halves"} += $line[ 5] / $reads * 1000000;
            $h->{"3p-CCA-tRFs"}  += $line[ 7] / $reads * 1000000;
            $h->{"3p-tRFs"}      += $line[ 9] / $reads * 1000000;
            $h->{"tRF-1"}        += $line[11] / $reads * 1000000;
            $h->{"tRNA-leader"}  += $line[13] / $reads * 1000000;
            $h->{"misc-tRFs"}    += $line[15] / $reads * 1000000;
        }
        close $trf;
        print Data::Dumper->Dump([\%hash], [qw/*hash/]);
        
        open my $merge, '>>', "$folder/merge"
            or die "$folder/merge: $!";
        my @tRF_types = ("5p-tR-halves", "5p-tRFs", "3p-tR-halves",
            "3p-CCA-tRFs", "3p-tRFs", "tRF-1", "tRNA-leader",
            "misc-tRFs");
        for my $tRNAname ( sort keys %hash ) {
            print $merge $tRNAname;
            for my $tRF_type (@tRF_types) {
                print $merge "\t$hash{$tRNAname}{$tRF_type}";
            }
            print $merge "\n";
        }
        close $merge;
    }
    close $dh;
}

[download]

For the sample data from this post, the output file merge I get is the following. Note that if you re-run the script, because of the append mode on the merge file, the same lines get added to that file again.

MT-TM    6500000    4500000    0    0    0    0    0    20416666.66666
+66
MT-TN    0    500000    0    0    0    750000    1000000    12625000
MT-TP    0    0    0    0    0    1000000    0    0
tRNA-Ala-AGC    0    3863095.23809524    0    0    136363.636363636   
+ 0    0    23353306.8783069
tRNA-Ala-CGC    0    8708333.33333333    0    0    0    14500000    50
+0000    8980291.00529101
tRNA-Ala-TGC    0    11833333.3333333    0    0    90909.0909090909   
+ 0    0    84521296.2962963
tRNA-Arg-ACG    0    100000    0    71428.5714285715    0    6500000  
+  0    4916666.66666667

[download]

Update: Minor edits and a few additions to the explanations.

In reply to Re^2: Skript help needed - RegEx & Hashes by haukex
in thread Skript help needed - RegEx & Hashes by PandaRaey

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