my $result = {
    'A' => {
        1 => 1,
        2 => 1,
        7 => 1,
       10 => 1,
       ...
    },    
    'B' => {
       ...
    },
    ...    
};

##</code><code>##

open my $fh, '<', $filename;

while (<$fh>) {
    chomp;
    my ($id, @numbers) = split;
    for my $number (@numbers) {
        $result->{$id}{$number} = 1;
    }
}

##</code><code>##

my %unique_numbers = ();
for (values %$result) {
    for my $number (keys %$_) {
       $unique_numbers{$number} = 1;
    }
}
my @numbers = sort {$a <=> $b} keys %unique_numbers;

open my $out_fh, '>', $output_filename;

print $out_fh "IDs @numbers\n";

for my $id (sort keys %$result) {
   my @fields = $id; 
   for my $number (@numbers) {
        if (exists $result->{$id}{$number}) {
           push @fields, 1;
        }
        else {
           push @fields, 0;
        }
   }
   my $string = join " ", @fields;
   print $out_fh "$string\n";
}