The code my $str = <STDIN>; graps "snape\n" - it includes the newline. That's the extra character. It's often helpful to print out your string, but do so in a way that shows hidden whitespace. I usually do it like this: print "str = [$str]\n"; - this puts brackets around it so that I can see if there are spaces or newlines at the end.

If I add chomp after the input for $str, I'm not getting any problem - I think you might be calling it as $str = chomp $str which is wrong. Just call chomp $str; like this:

#!/usr/bin/perl -w

use strict;
use warnings;

print "Enter the string =";
my $str = <STDIN>;
chomp $str; #### here is the call to chomp
print "Enter the size =";
my $n = <STDIN>;
print "The Length of the string = ",length($str);

if ($n <= length($str)){
my $x = pretty_print($str,$n);
print "\nThe substring is =  ",$x;
}

else{
print"\nThe length of the string is shorter than the size ";
}

sub pretty_print{
my ($dna,$len) = @_;
my $substring = substr($dna,0,$len);
return $substring;
}
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So close :-)