Find nucleotides in DNA sequence with perl - perl

Question

I have the sequence DNA and I want to find nucleotide of the sequence at the position which was chosed by people. Below is the example:
Enter the sequence DNA:
ACTAAAAATACAAAAATTAGCCAGGCGTGGTGGCAC (the length of sequence is 33)
Enter the position: (12)
I hope the result is the position number 12 the nucleotides are AAA.
I have no problem finding the amino acid of the position. Below is the current code I have.
print "ENTER THE FILENAME OF THE DNA SEQUENCE:= ";
$DNAfilename = <STDIN>;
chomp $DNAfilename;
unless ( open(DNAFILE, $DNAfilename) ) {
print "Cannot open file \"$DNAfilename\"\n\n";
}
#DNA = <DNAFILE>;
close DNAFILE;
$DNA = join( '', #DNA);
print " \nThe original DNA file is:\n$DNA \n";
$DNA =~ s/\s//g;
print" enter the number ";
$po=<STDIN>;
#pos=$DNA;
if ($po>length($DNA))
{
print" no data";
}
else
{
print " #pos\n\n";
}
Please advice how can I find the position at the DNA sequence.

Answer 1

my $nucleotide = substr $DNA, $po, 3;
This will take the 3 nucleotides from positions $po upto $po+2 and assign it to $nucleotide.

Answer 2

That'll be something like this:
use strict;
use warnings;
print 'ENTER THE FILENAME OF THE DNA SEQUENCE:= ';
my $DNA_filename = <STDIN>;
chomp $DNA_filename;
unless (open(DNAFILE, $DNA_filename))
{
die 'Cannot open file "' . $DNA_filename . '"' . "\n\n";
}
my #DNA = <DNAFILE>;
close DNAFILE;
my $DNA_string = join('', #DNA);
print "\n" . 'The original DNA file is:' . "\n" . $DNA_string . "\n";
$DNA_string =~ s/\s//g;
print ' enter the number ';
my $pos = <STDIN>;
if ($pos > length($DNA_string))
{
print ' no data';
}
else
{
print ' ' . substr($DNA_string, $pos, 3) . "\n\n";
}
Some comments:
Always use strict and use warnings - it'll help you to write better and bug-free code.
I personally don't like using interpolation in double quoted strings, hence those concatenations.
Result's position is starting with 0 - if you want, you may change last if's condition and else.
Edit: I've misread part of question about nucleotides, as #hexcoder wrote, you want substr($DNA_string, $pos, 3).