in reply to Find element in array

Unlike the "C" language, Perl strings are much different from arrays. In Perl, you usually have a choice of which to use. String solutions are usually easier and almost always execute faster. Here is a string-only solution to your problem. 
use strict;
use warnings;

my $DNA = "ATATCCCGATCAGG3TT!GCA\n";
chomp $DNA;
print "The length of the sequence is:\n", length($DNA), "\n";

my $nucleotideDNA = $DNA;
#my $count = $nucleotideDNA =~ tr/ATCG]//c;  # Remove and count invali
+ds
my $count = $nucleotideDNA =~ tr/ATCG//cd;  # Remove and count invalid
+s

my $locations;  # Find location of invalids in original string
$locations  .=  "$-[0], " while ( $DNA =~ /[^ATCG]/g );

print "There are $count non-valid nucleotides at locations:\n$location
+s \n";


OUTPUT:
The length of the sequence is:
21
There are 2 non-valid nucleotides at locations:
14, 17,

[download]

UPDATE: Modified one line of code to correct errors identified by AnomalousMonk (below) Original remains as comment.

Bill

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Re^2: Find element in array
by AnomalousMonk (Archbishop) on Feb 17, 2020 at 06:23 UTC
    my $count = $nucleotideDNA =~ tr/ATCG]//c;  # Remove and count invalids

    Sofie:   Note that while this  tr/// (see Quote-Like Operators in perlop) expression counts the number of characters that are not ATCG, it does not remove anything; the string is not changed (update: nor is there any need for change): 

    c:\@Work\Perl\monks>perl -wMstrict -le
"my $DNA = 'ATATCCCGATCAGG3TT!GCA';
 ;;
 my $nucleotideDNA = $DNA;
 my $count = $nucleotideDNA =~ tr/ATCG//c;
 ;;
 print $DNA;
 print $nucleotideDNA;
 ;;
 print 'sequences are equal' if $DNA eq $nucleotideDNA;
"
ATATCCCGATCAGG3TT!GCA
ATATCCCGATCAGG3TT!GCA
sequences are equal

    [download]
    Also note that there is a  ] character in the set |  tr/// search set that should not be there.

    However, I agree with the main point that BillKSmith is making: string operations with regexes or with operators like substr and index will tend to be significantly faster (update: and to consume significantly less memory) than equivalent array operations.

    Give a man a fish:  <%-{-{-{-<

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