$VAR1 = {
          '315' => {
                     '8' => 0
                   },
          '329' => {
                     '6' => 0
                   },
          '352' => {
                     '5' => 0
                   },
          '390' => {
                     '1' => 0
                   },
          '280' => {
                     '7' => 1
                   },
          '360' => {
                     '9' => 0
                   },
          '349' => {
                     '4' => 0
                   },
          '305' => {
                     '10' => 0
                   },
          '380' => {
                     '3' => 1
                   },
          '251' => {
                     '2' => 0
                   }
        };

##</code><code>##

sample  1   2   3   4   5   6   7   8   9   10
file1   0   0   1   0   0   0   1   0   0   0

##</code><code>##

my %output=();
foreach my $k1(keys %pos2base2bin){
    foreach my $k2 (sort{$a <=> $b} keys %{ $pos2base2bin{$k1} }){
        push @{$output{$k2}},$pos2base2bin{$k1}{$k2}
    }
}

my @array=();
foreach my $k(sort{$a <=> $b} keys %output){
    foreach my $val(@{$output{$k}}){
        push @array,$val;
    }
}

print join("\t",$f,@array),"\n"; # $f is the filename