# populate DISTINCT ids from table into a variable
# separated by pipe symbol; variable looks like below
# and contains 15000 distinct ids
$compare = "F1|FTDR|RJIER|KERF...." 

# open the file and loop
open (MFIL,"<datafile") or die ("ouch");
while ($lines = <MFIL>)
{
  chomp ($lines);
  $lines =~ m/^$compare/o && next;
  print $lines,"\n";
}
close (MFIL);