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

my $infile = $ARGV[0];
my $infile2 = $ARGV[1];

unless (open(INFILE, $infile)){
       die "Couldn't open infile: $!\n";
}


my @AtypeData = qw(A0101 A0102 A0201 A0202 A0205 A0301 A0302 A1101 A2301 A2402 A2403 A2601 A2608 A2902 A3001 A3002 A3004 A3101 A3201 A3601 A6801 A6802);


my %diplotypes;
my %diplotypes2;

initHash(\%diplotypes, \@AtypeData);
initHash(\%diplotypes2, \@AtypeData);

##read in the data
while (<INFILE>){
	chomp;
	my @line = split ('\t', $_);
	my $key1 = 'A' . $line[0] . '.' . 'A' . $line[1]; ##first key
	my $key2 = 'A' . $line[1] . '.' . 'A' . $line[0]; ##key the other way
	##check to see if the key exists in the hash
	 ##if it doesn't there is data in your infile, not in you names array
	if (exists $diplotypes{$key1} && $line[0] <= $line[1]) {
		$diplotypes{$key1} += $line[2];
		}
	elsif (exists $diplotypes{$key2} && $line[0] >= $line[1]) {
		$diplotypes{$key2} += $line[2];
		}
	else{##world is out to get you
		print STDERR "No key for $key1 or $key2\n";
		next;
	}

}

close INFILE;

unless (open(INFILE2, $infile2)){
       die "Couldn't open infile: $!\n";
}
while (<INFILE2>){
	chomp;
	my @line = split ('\t', $_);
	my $key1 = 'A' . $line[0] . '.' . 'A' . $line[1]; ##first key
	my $key2 = 'A' . $line[1] . '.' . 'A' . $line[0]; ##key the other way
	##check to see if the key exists in the hash
	 ##if it doesn't there is data in your infile, not in you names array
	if (exists $diplotypes2{$key1} && $line[0] <= $line[1]) {
		$diplotypes2{$key1} += $line[2];
		}
	elsif (exists $diplotypes2{$key2} && $line[0] >= $line[1]) {
		$diplotypes2{$key2} += $line[2];
		}
	else{##world is out to get you
		print STDERR "No key for $key1 or $key2\n";
		next;
	}

}
foreach my $key1(keys %diplotypes){
		if (exists $diplotypes2{$key1}){
			$diplotypes{$key1} /= $diplotypes2{$key1} +0.01;
			}
		}




close INFILE2;

printData(\%diplotypes, \@AtypeData);

sub initHash {  #init the all to all hash
	##first argument is the hash of data, and the second is a reference to all the columns
	my ($refHash, $refArr) = @_;
	foreach my $ele1(@$refArr){
		foreach my $ele2(@$refArr){
			my $key = $ele1 . "." . $ele2;

			if (exists $$refHash{$key}){
				print STDERR "This key existed in your array of names, skipping\n";
				next;
			}
			else{
				$$refHash{$key} = 0;
			}
		}
	}
}
sub printData {
	
	my ($refHash, $refArr) = @_;
	#print header line;
	print "MATRIX\t";
	foreach my $ele(@$refArr){
		print "$ele", "\t";
	}
	print "\n";
	#print out the actual data	
	foreach my $ele1(@$refArr){
		print "$ele1" , "\t";##print out the first value on the row, which is the name
		foreach my $ele2(@$refArr){
			my $key = $ele1 . "." . $ele2;
			if (exists $$refHash{$key}){
				printf "%.2f \t", $$refHash{$key};
			}
			else{
				print STDERR "Something is wrong\n";
			}
		}
		print "\n";
	}

	
}