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my $str = do {my $i; join "", map {$_ eq '(' ? $i++ : $_ eq ')' && $i 
+? $i-- : $_ eq ',' && $i ? ($_ = ';') : 0; $_} split '[(,)]', $str};

    "(foo),(bar)"

substr($str, index($str, "("), rindex($str, ")") - length($str)) =~ s/
+,/;/g;