Hello GSperlbio,

Yet another option is to use the core Tie::File module:

#! perl
use strict;
use warnings;
use Tie::File;

my $data = 'uuu.txt';

tie my @lines, 'Tie::File', $data
    or die "Cannot tie file '$data': $!";

s{[^ACGT]}{}g for @lines;

untie @lines;
[download]

But note that this will not remove newlines.

Hope that helps,