#### One big regex ####
## don't do this and the previous

## read in file
my $ptt_file="/g/Viruses/prophage_data/prophage_region.ptt1";
open ($fh, '<', $ppt_file);
@lines = <$fh>;
close ($fh);
$text = join ('', @lines);

## you don't need to precompile this -- it's for clarity
## and in case you ever want to remove these from multiple
## files, i.e., put it in a loop
## Again, I assume the geneid is at the front of the line.
my $saved_lines = '';
my $rx_rm_lines = qr/
  (^(\w+).+$ [\r\n])
  (?{
    if (! exists $geneids_to_remove->{$2})
    {
      $saved_lines .= $1;
    }
  })
/xm; # the 'm' modifier enables multiline regex

## run the regex (you can use s/.../$1/g if you
## don't want to destroy the string as you search
$text =~ s/$rx_rm_lines//g;