If you're dealing with a known set of tokens (i.e. numbers), you could just search for each in turn.

my $string = '1,3,5,7,9,1,3,4,5,6,2,1,5,6,7,9';

for my $num (1..9) {
   my $count = () = ",$string," =~ /,$num(?=,)/g;
   print "$num\t$count\n";
}
[download]

1       3
2       1
3       2
4       1
5       3
6       2
7       2
8       0
9       2
[download]

The general solution of using a hash is probably better, though.

my $string = '1,3,5,7,9,1,3,4,5,6,2,1,5,6,7,9';

our %counts;
my $x = "$string,";
1 while $x =~ /([^,]*),(?{ $counts{$1}++ })/g;

for my $num (sort { $a <=> $b } keys %counts) {
   print "$num\t$counts{$num}\n";
}
[download]

1       3
2       1
3       2
4       1
5       3
6       2
7       2
9       2
[download]