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## open the file and read in data
my $list_file = '/g/Viruses/prophage_data/emptySeqList_aa.txt'; 
...
    $geneids_to_remove->{$1} = 1; # store geneids in a hash
  })
//gx;

#### Per line ####
my $ptt_file="/g/Viruses/prophage_data/prophage_region.ptt1";
...
  }    
}
close ($fh);

#### One big regex ####
## don't do this and the previous
...
## don't want to destroy the string as you search
$text =~ s/$rx_rm_lines//g;

## write out saved data
open ($fh, '>', $outfile);
print $fh $saved_lines;
close ($fh);