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,
UPDATE: Modified one line of code to correct errors identified by AnomalousMonk (below) Original remains as comment.
-
Are you posting in the right place? Check out Where do I post X? to know for sure.
-
Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
<code> <a> <b> <big>
<blockquote> <br /> <dd>
<dl> <dt> <em> <font>
<h1> <h2> <h3> <h4>
<h5> <h6> <hr /> <i>
<li> <nbsp> <ol> <p>
<small> <strike> <strong>
<sub> <sup> <table>
<td> <th> <tr> <tt>
<u> <ul>
-
Snippets of code should be wrapped in
<code> tags not
<pre> tags. In fact, <pre>
tags should generally be avoided. If they must
be used, extreme care should be
taken to ensure that their contents do not
have long lines (<70 chars), in order to prevent
horizontal scrolling (and possible janitor
intervention).
-
Want more info? How to link
or How to display code and escape characters
are good places to start.
|