#!/usr/bin/perl

use strict;
use warnings;

$/ = undef;     # slurp-mode for input, just in case
while ( <> ) {  # reads stdin or all file names in ARGV
    s/\s+//g;   # remove whitespace
    my $content = $_;  # keep a working copy
    tr/ACGTacgt//d;    # remove all acgt

    if ( length() ) { # anything left?
        print "$ARGV bad content: $_\n";
        do_something_with_bad_data( $ARGV, $content );
    } else {
        print "$ARGV all clean!\n";
        do_something_with_good_data( $ARGV, $content );
    }
}

sub do_something_with_bad_data
{
    my ( $filename, $data ) = @_;
# . . . fix it?  report it to someone?
}

sub do_something_with_good_data
{
    my ( $filename, $data ) = @_;
# . . . whatever you want to do
}