X	Y	A	B	Q	PA	PB
N	r	C	T	0.936	0.057	0.936
...

#!/usr/bin/perl
use warnings;

my $file = "test.txt";
my @x;
my @id;
my @marker;
my @allelA;
my @allelB;
my @quality;
my @probA;
my @probB;
my $laenge_x;

my $file_mach = "test2.txt";
my @mach;
my @id_mach;
my @marker_mach;
my @allelA_mach;
my @allelB_mach;
my @quality_mach;
my @probA_mach;
my @probB_mach;
my $laenge_mach;


open( IN, "<$file" ) or die "Konnte Input nicht oeffnen!\n";
	while (<IN>) {
		chomp($_);
		@x = split(/\t/, $_ );
		push(@id, $x[0]);
		push(@marker, $x[1]);
		push(@allelA, $x[2]);
		push(@allelB, $x[3]);
		push(@quality, $x[4]);
		push(@probA, $x[5]);
		push(@probB, $x[6]);

	}

close(IN);

open (IN2, "<$file_mach");
while (<IN2>) {
		chomp($_);
		@mach = split(/\t/, $_ );
		push(@id_mach, $mach[0]);
		push(@marker_mach, $mach[1]);
		push(@allelA_mach, $mach[2]);
		push(@allelB_mach, $mach[3]);
		push(@quality_mach, $mach[6]);
		push(@probA_mach, $mach[4]);
		push(@probB_mach, $mach[5]);

	}

close(IN2);

my $together = 0;
my $mach = 0;
my $x = 0;
for my $i (1..$#id){
	for my $j (1..$#id_mach){
		if ( $id[$i] eq $id_mach[$j] and
			 $marker[$i] eq $marker_mach[$j] and
			 $allelA[$i] eq $allelA_mach[$j] and
			 $allelB[$i] eq $allelB_mach[$j])
		{
			$together++;
		}
	
	}
	
}
print $together;