I thought I'd provide another solution. It uses a hash, %seen, to serve as a lookup for genes in 'HFR_genes.txt' that are also in 'gene_list.txt'.

#!/usr/bin/perl
use 5.010;
use strict;
use warnings;

my $gene_list = 'gene_list.txt';
open GL, "<", $gene_list or die "Unable to open $gene_list because $!"
+;

my %seen;
while (my $gene = <GL>) {
    $seen{$gene}++;
}
close GL or die "Unable to close $gene_list because $!";

my $hfr = 'HFR_genes.txt';
open HFR, "<", $hfr or die "Unable to open $hfr because $!";

while (my $gene = <HFR>) {
    print if $seen{$gene};
}
close HFR or die "Unable to close $hfr because $!";
[download]

Chris

Update: If both files have unique lines, the code could be shortened to:

my %seen;
print grep $seen{$_}++, <>;
[download]

With the command line supplying the 2 files: perl your_program.pl gene_list.txt HFR_genes.txt