open my $fh, '<', $file or die "Can't read $file: $!";

##</code><code>##

		my $start = $1; $start--; #increment down for substr
		my $end = $2; $end--; #increment down for substr

##</code><code>##

sub html_out {
    my ( $total_muts, $mutant_genes_ref ) = @_;

    my %mutant_genes = %{$mutant_genes_ref};
    # ...etc...
}