Maybe this will do:

use strict;
use warnings;

my @id1 = (1..5);
my @id2 = (11..15);

my %hash;
my %col_header;
my %row_header;

my $last = $#id1 > $#id2 ? $#id1 : $#id2;

for my $i (0..$last) {
    if ( defined( $id2[$i] ) ) {
        $col_header{$id2[$i]} = 1;
    }
    if ( defined( $id1[$i] ) ) {
        $row_header{$id1[$i]} = 1;
    }
    if ( defined( $id1[$i] ) and defined( $id2[$i] ) ) {
        $hash{$id1[$i]}{$id2[$i]} = 1;
    }
}

my @col_header = sort numeric keys %col_header;
my @row_header = sort numeric keys %row_header;

printf "%10s" x (@col_header + 1), "id1\\id2", @col_header;
print "\n";

for my $row ( @row_header ) {
    printf "%10s", "$row";
    for my $col ( @col_header ) {
        printf "%10s", ( exists( $hash{$row}{$col} ) ? "1" : "0");
    }
    print "\n";
}

sub numeric {
    $a <=> $b;
}
[download]

with output:

   id1\id2        11        12        13        14        15
         1         1         0         0         0         0
         2         0         1         0         0         0
         3         0         0         1         0         0
         4         0         0         0         1         0
         5         0         0         0         0         1
[download]

(I'll leave it to OMAR to turn this into a sub.)

Update: here's the read-from-STDIN version:

use strict;
use warnings;

my $pair_name;
while (<>)
{
    $pair_name = join '\\', split;
    last;
}

my %hash;
my %col_header;
my %row_header;

while (<>)
{
    my @pair = split;
    $hash{$pair[0]}{$pair[1]} =
    $row_header{$pair[0]} =
    $col_header{$pair[1]} = 1;
}

my @col_header = sort numeric keys %col_header;
my @row_header = sort numeric keys %row_header;

printf "%10s" x (@col_header + 1), $pair_name, @col_header;
print "\n";

for my $row ( @row_header ) {
    printf "%10s", "$row";
    for my $col ( @col_header ) {
        printf "%10s", ( exists( $hash{$row}{$col} ) ? "1" : "0");
    }
    print "\n";
}

sub numeric {
    $a <=> $b;
}
[download]