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

##</code><code>##

{
  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 },
}

##</code><code>##

$analyse{$animal_color}{$animal_name}{$animal_type}++
          if defined $animal_color;

##</code><code>##

$analyse{$animal_color}{$animal_type}++
          if defined $animal_color;

##</code><code>##

{
  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 },
}