#!/usr/bin/perl
use strict;
use warnings;

my %data;
while (<DATA>) {
	chomp;
	my (undef, $sample, @fields) = split /[\t;]/;
	
	for (@fields) {
		my ($type, $value) = split /__/;
		$data{$type}{$sample}{$value}++ if $value;	
	}
}

for my $type (keys %data) {
	my $entity = $data{$type};
	my @samples = sort keys %$entity;
	
	my %seen;
	my @keys = grep !$seen{$_}++, map keys %$_, values %$entity;
	
	open my $fh, '>', "$type.csv" or die "Unable to create '$type.csv'. $!";
	
	print $fh join(",", ' ', @samples), "\n";
	for my $key (@keys) {
		print $fh join(",", $key, map $entity->{$_}{$key} || 0, @samples), "\n";
	}
	
	close $fh or die "Unable to close '$type.csv'. $!";
}

__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>##

C:\Old_Data\perlp>type a.csv
 ,A,B,C
bear,6,2,6
wolf,4,7,5

C:\Old_Data\perlp>type c.csv
 ,A,B,C
white,1,0,1
black,1,0,1
brown,3,1,4
red,1,1,0
grey,1,5,3

##</code><code>##

C:\Old_Data\perlp>perl t5.pl
$VAR1 = {
          'c' => {
                   'A' => {
                            'white' => 1,
                            'black' => 1,
                            'brown' => 3,
                            'red' => 1,
                            'grey' => 1
                          },
                   'C' => {
                            'white' => 1,
                            'black' => 1,
                            'brown' => 4,
                            'grey' => 3
                          },
                   'B' => {
                            'red' => 1,
                            'brown' => 1,
                            'grey' => 5
                          }
                 },
          'a' => {
                   'A' => {
                            'bear' => 6,
                            'wolf' => 4
                          },
                   'C' => {
                            'bear' => 6,
                            'wolf' => 5
                          },
                   'B' => {
                            'bear' => 2,
                            'wolf' => 7
                          }
                 }
        };