## open the file and read in data
my $list_file = '/g/Viruses/prophage_data/emptySeqList_aa.txt'; 
  ## try to use single quotes when 
  ## you don't need string interpolation,
  ## e.g., no variables or "\n"
open (my $fh, '<', $list_file); 
  ## it is often preferable to use a
  ## variable to store a filehandle
my @lines = <$fh>; # reads entire file in one go
  ## This is technically bad form, 
  ## but assuming your file isn't too big, it's fine
close ($fh);
my $text = join ('', @lines); # combines all lines into one string

## Here's where your file format will change the code
## I'm assuming nothing is in the file but gene ids,
## and that each id consists of letters, numbers, and underscores.
## This regex will identify all geneids (using \w+)
## and store them as hash keys.
my $geneids_to_remove = {}; # create a hash reference
$text =~ s/(\w+)
  (?{ # in regex code
    $geneids_to_remove->{$1} = 1; # store geneids in a hash
  })
//gx;