Here's how I would modify the OP script: 
#!/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
    tr/ACGTacgt//d; # remove all acgt

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

[download]
Using  while (<>) is good (even with slurp-mode input) because that way you can pipe data from any other process as input to the script, or you can put one or more file names on the command line (e.g. "*.txt").

When you read multiple input files in one run, putting "$ARGV" in the print statements tells you which files are good or bad.

In reply to Re: =~ matches non-existent symbols by graff
in thread =~ matches non-existent symbols by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.