Hi ejohnston7,

Hash to the rescue... Using the data given by the OP. One can do like so:

use warnings;
use strict;

my %analyse;

while (<DATA>) {
    chomp;
    if ( my ( $animal_type, $animal_name, $animal_color ) =
        m/.+?([A-Z]).+?__(.+?);.+?__(.+?)?$/ )
    {
        $analyse{$animal_name}{$animal_type}++;
        $analyse{$animal_color}{$animal_name}{$animal_type}++
          if defined $animal_color;
    }

}

use Data::Dump;
dd \%analyse;

__DATA__
occurence1    A    a__bear;c__black
occurence2    B    a__wolf;c__grey
occurence3    A    a__wolf;c__white
occurence4    A    a__bear;c__
occurence5    C    a__wolf;c__grey
occurence6    C    a__bear;c__brown
occurence7    A    a__wolf;c__
occurence8    B    a__wolf;c__
occurence9    C    a__bear;c__black
occurence10    C    a__wolf;c__
occurence11    A    a__wolf;c__red
occurence12    B    a__wolf;c__grey
occurence13    C    a__wolf;c__grey
occurence14    C    a__wolf;c__grey
occurence15    B    a__bear;c__brown
occurence16    C    a__bear;c__brown
occurence17    A    a__bear;c__
occurence18    A    a__bear;c__brown
occurence19    C    a__wolf;c__white
occurence20    B    a__wolf;c__grey
occurence21    B    a__bear;c__
occurence22    B    a__wolf;c__grey
occurence23    A    a__wolf;c__grey
occurence24    A    a__bear;c__brown
occurence25    C    a__bear;c__brown
occurence26    A    a__bear;c__brown
occurence27    C    a__bear;c__
occurence28    C    a__bear;c__brown
occurence29    B    a__wolf;c__red
occurence30    B    a__wolf;c__grey
[download]

The output shows the two tables together. The desired output is left for the OP to make happen.
Output from the code above:

{
  bear  => { A => 6, B => 2, C => 6 },
  black => { bear => { A => 1, C => 1 } },
  brown => { bear => { A => 3, B => 1, C => 4 } },
  grey  => { wolf => { A => 1, B => 5, C => 3 } },
  red   => { wolf => { A => 1, B => 1 } },
  white => { wolf => { A => 1, C => 1 } },
  wolf  => { A => 4, B => 7, C => 5 },
}
[download]

Update:
And if you just care about just getting the color, with the frequency of type, then you can change this:

$analyse{$animal_color}{$animal_name}{$animal_type}++
          if defined $animal_color;
[download]

to this

$analyse{$animal_color}{$animal_type}++
          if defined $animal_color;
[download]

then your output would be:

{
  bear  => { A => 6, B => 2, C => 6 },
  black => { A => 1, C => 1 },
  brown => { A => 3, B => 1, C => 4 },
  grey  => { A => 1, B => 5, C => 3 },
  red   => { A => 1, B => 1 },
  white => { A => 1, C => 1 },
  wolf  => { A => 4, B => 7, C => 5 },
}
[download]