[Aa]tom[oi]:[Nn]ucle[oi]
[Nn]ucle[oi]:[Pp]roton[ei]
[download]

OK. So the core of what you have:

  while (my $text=<$testo>){
    for my $key (keys %hash){
      my $value = $hash{$key};
      my $arrkey=$key." ";  
      my $count = 0;
      $count += () = /\b$key\b/ig while <>;
      print $conteggio "$arrkey) => $count\n";
    } ;
  } ;
[download]

reads the file line by line into $text, and then tries each column 1 word (captured earlier as the key values in your %hash). The regex /\b$key\b/ig is plausible, and the [oi] stuff will do what you want -- the [Nn] will also work, but are redundant because of the i qualifier of the regex.

The rest is, frankly, a dogs breakfast and can be thrown away.

To count the number of times you get a match in each line,

  my $count = () = $text =~ /\b$key\b/ig ;
[download]

is sufficient, but fairly deep magic. This:

  my $count = 0 ; while ($text =~ /\b$key\b/ig) { $count++ ; } ;
[download]

may or may not seem clearer.

Now your problem is how to collect the count for each word across all the lines of your input. I suggest using the value part of your hash entries to hold the count for the word in the key part.

When the while loop has finished, your hash should contain the count for each word, which you can then output to $coteggio.

thanks! It's working fine now! I'll post the code I used, so you all can give me suggestion for improving my programming skills (I'm sorry if they're not good, but I've been using Perl for just a few week, for my Thesis, and it's all really new), or maybe it could be useful for someone with the same problem..


open my $testo, "<File_Input/Testo.txt";  
open my $conteggio, ">File_Output/Conteggio.txt";
my %arrayris;


    while (my $text=<$testo>){
     for my $key (keys %hash){
     my $value = $hash{$key};
     my $count = 0 ; 
     while ($text =~ /\b$key\b/ig) { $count++ ; } ;
     $arrayris{$key}=$count;


      
}
}

while ( my ($k,$v) = each %arrayris ) {
    print $conteggio "($k) => $v\n";
  
}
close $testo;
close $conteggio;
[download]


Thanks again, to everybody!

If you can not figure out what some code is doing, you could break it up into smaller, isolated chunks (i.e., subs):

use strict;
use warnings;

my %patts;
my %counts;

my $file = 'patterns.txt';
my $fh;
open $fh, '<', $file or die "can not open file $file: $!";
while (<$fh>) {
    chomp;
    my ($word1, $word2) = split /:/;
    $patts{$word1} = $word2;
}
close $fh;

$file = 'text.txt';
open $fh, '<', $file or die "can not open file $file: $!";
while (<$fh>) {
    chomp;
    for my $patt (keys %patts) {
        $counts{$patt} += count_match($_, $patt);
    }
}
close $fh;

for my $patt (keys %counts) {
    print "pattern $patt occurs $counts{$patt} times\n";
}

sub count_match {
    my ($str, $regex) = @_;
    my @words = split /\s+/, $str;
    my $count = 0;
    for (@words) { $count++ if /\b$regex\b/ }
    return $count;
}

__END__
pattern [Aa]tom[oi] occurs 1 times
pattern [Nn]ucle[oi] occurs 3 times
[download]