I saw Not_a_Number's solution as I was about to post mine. I've added his extra test data plus an additional one of my own which has nothing in either column 2 or 3.

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;

my %result;

while (<DATA>) {
    map {
        $result{$_->[0]}[0] += defined $_->[1] && $_->[1] eq q{1_x} ? 
+1 : 0;
        $result{$_->[0]}[1] += defined $_->[2] ? 1 : 0;
    } ([split]);
}

say qq{$_ }, join q{,} => @{$result{$_}} for sort keys %result;

__DATA__
A 1_x 9_z
A 1_x 
A 1_x g_z
B 2_c 
B 1_x 1_z
C 1_x 1_z
C v_x 8_z 
D v_x s_x
E 1_x
F
[download]

This outputs:

$ pm_extract_1_x.pl
A 3,2
B 1,1
C 1,2
D 0,1
E 1,0
F 0,0
[download]