use strict;
my $str = 'Almonds ; Roasted Peanuts (Peanuts; Canola Oil (Antioxidants (319; 320)); Salt); Cashews
Peanuts (32.5%); Macadamia Nuts (14%; PPPG(AHA)); Hazelnuts (9%); nuts(98%)';
my $regex = qr/[^;]*(\((?>[^()]+|(?1))*\))(*SKIP)(*F)|;/mp;
my $subst = ',';
my $result = $str =~ s/$regex/$subst/rg;
print "The result of the substitution is' $result\n";
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Perl, please visit: http://perldoc.perl.org/perlre.html