use strict;
use warnings;


my @data; # this will be an array of arrays
while(<DATA>) # read from __DATA__ for simplicity
{
    chomp;
    if($_ eq '<sep>') { push @data, [] }
    else              { push @{$data[-1]}, $_ }
}

foreach (@data) {
    print "<sep>\n", join("\n", sort { $a <=> $b } @$_), "\n";
}

__DATA__
<sep>
22
1
3
<sep>
4
2
44
[download]

<sep>
1
3
22
<sep>
2
4
44

Tool completed successfully
[download]