I think we should benefit from Perl 5.6's (??{ ... }) regex expression.

$REx = qr{
  \(
  (?:
    (?> [^()]+)
    |
    (??{ $REx })
  )*
  \)
}x;
$str =~ s/($REx)/(my $a = $1) =~ tr!;!,!; $a/eg;
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This makes it work for nested parens, too, like "hi; there; (fools; (all))"