I altered your script so that it would just work. The biggest problem that I encountered was getting around the illegal divsion by zero such as:

$precision = $feature_found / $rank;
[download]

What I did:

$precision = eval { 
    $feature_found ? $rank / $feature_found : 0; };
[download]

Here's the script:

#!/usr/bin/perl

use strict;
use autodie;
use Devel::SimpleTrace;
use Data::Dumper::Concise;

my $input       = shift @ARGV;
my $input_bless = '';
my $log         = '/root/Desktop/log.txt';

die $! unless open IN,  '<', $input;
die $! unless open OUT, '>', $log;

my %matrice;
while ( defined( $_ = <IN> ) ) {
    my ( $rank, $nome, $relaz, $entry2, $score ) = split( ' ', $_, 6 )
+;
    push @{ $matrice{$nome}; }, "${relaz}_$entry2,$rank,$score";
}

my %HOH;
while ( my ( $name, $aref ) = each %matrice ) {
    do {
        foreach my $item (@$aref) {
            my ( $prop, $rank, $score ) = split( /,/, $item, 4 );
            $HOH{$name}{$prop} = "$rank,$score" || 0;
        }
    };
}

die unless open INB, '<', $input;
while ( defined( $_ = <INB> ) ) {
    my ( $u, $superclass, $rel, $v ) = ( 
      split( ' ', $_, 0 ) )[ 0, 1, 2, 3 ];
    my $conteggio = &calcolo( $u, $v );
    print OUT "$u" . "\t" . $rel . "\t" . $v . "\t" . $conteggio;
}

sub calcolo {
    my ( $name1, $name2 ) = @_;
    my $first  = $HOH{$name1};
    my $second = $HOH{$name2};
    my ( $rank_fv, $score_fv );
    my $rank_v;
    my $count_feat_fv;
    my $provaprec = 0;
    my $proptoexamine;
    my $count_feat_rel;
    my $precision;
    my $rel_par;
    my $num = 0;
    my $count_feat_fu;
    my $apinc;
    my $rank2 = 0;
    my ( $prop, $score );
    my $rank          = 0;
    my $feature_found = 0;
    my $feat_finale;
    my $rel_to_sum;

    while ( my ( $name1, $aref ) = each %matrice ) {
        ++$count_feat_fu;
        $num = 0;
        my $feat_rel = 0;
        foreach my $item (@$aref) {
            ( $prop, $rank, $score ) = split( /,/, $item, 4 );
            $feat_finale = &last_el_v( $name2, $prop );
            while ( my ( $prop1, $rankscore1 ) = each %$second ) {
                ($rank_fv, $score_fv ) = split( /,/, $rankscore1, 3);
                if ( $prop1 eq $prop ) {
                    ++$feature_found;
                    print 'PROP:' . $prop . "\n";
                    print "TROVATO" . "\n";
                    ++$feat_rel;
                    $rank2 = $rank_fv;
                    print 'RANK 2:' . $rank2 . "\n";
                    print 'RANK 1: ' . $rank . "\n";
                    print 'COUNT FEAT FOUND: ' . $feature_found . "\n"
+;
                    $precision = eval {
                      $feature_found ? $rank / $feature_found : 0; };
                    print 'PRECISION: ' . $precision . "\n";
                    $rel_par = $rank2 / ( $feat_finale + 1 );
                    $rel_to_sum = 1 - $rel_par;
                    print 'FEAT FINALE: ' . $feat_finale . "\n";
                    print 'REL PAR: ' . $rel_par . "\n";
                    
                    my $tosum = $precision * $rel_to_sum;
                    print 'TO SUM: ' . $tosum . "\n";
                    $num = $num + $tosum;
                    print 'NUM: ' . $num . "\n";
                    }
                };
            }
            print 'RANK: ' . $rank . "\n";
            $apinc = eval { $num ? $rank / $num : 0; };
            print 'APINC: ' . $apinc . "\n";
            return $apinc;
    };
}

sub last_el_v {
    my ( $name2, $prop1 ) = @_;
    my $second = $HOH{$name2};
    my $count_feat_fv;
    while ( my ( $prop1, $rankscore1 ) = each %$second ) {
        ++$count_feat_fv;
    };
    return $count_feat_fv;
}
close IN;
close INB;
close OUT;
[download]

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.