my @sth;

while (<DATA>) {
  my @id = split /,/, $_;

  $sth[@id] ||=
    $dbh->prepare(
      'SELECT id, size FROM table WHERE id IN (' .
      join(',', ('?') x @id) . ')'
    );
  $sth[@id]->execute(@id);
  while (my($id, $size) = $sth[@id]->fetchrow_array()) {
    print "$id $size\n";
  }
}
__DATA__
1,4,6
7,10
9
2,5,8
3