#!/usr/bin/perl -w
use strict;
my $dinu_r;
my $energy;
my @energy1;
my @energy2;
my @energy3;
my @energy4;
my @energy5;
my $i;
for (my $x=1; $x<=5; $x++)
{
open (AA, "shuffle$x")or die "Can't open input  ($!)\n"; # LINE A

my $Sequence;
   $i=length($Sequence);
while (<AA>)
{
  $Sequence=$_;
}
close(AA);

my %Winenergy = Energy($Sequence,$dinu_r);
open (OUT, ">shuffle$x.stb");  # LINE B

foreach my $el1(sort{$a <=> $b} keys %Winenergy)
{
  push(@energy.$x , $Winenergy{$el1}); #LINE C
#  print OUT "$el1\t $Winenergy{$el1}\n";
}
#print OUT "\n";
close (OUT);
}

 sub Energy{

my ($sequence,$dinu_r) = @_;
my %dinu = %$dinu_r;
my $frame=1;
my $win=15;
my $lensequence = length($sequence); #length of the genome sequence
my $limit1 = $lensequence-$win+1; #no of windows
my $wincenpos = 1+($win-1)/2; #centre postion for the first window
my %winenergy = ();
my $j = 0; #starting position of the window
while($j<$limit1)
{
  my $winseq = substr($sequence,$j,$win);
  my $energy = 0;
  for(my $k =0; $k < $win-1; $k++)
  {
    my $dinucle_temp = substr($winseq,$k,2);
    my $dinucle = uc($dinucle_temp);
    $energy = $energy + $dinu{$dinucle};
  }#end for $k
  my $wincentre = $j+$wincenpos;
   $winenergy{$wincentre} = $energy;
  $j = $j+$frame;
}#end for $j
return %winenergy;
}
open(FILE,">total_shuffle.stb");
my $m=8;
for(my $j=0;$j<$i;$j++)
{
my $avg = ($energy1[$j]+$energy2[$j]+$energy3[$j]+$energy4[$j]+$energy
+5[$j])/5;
        print FILE "$m\t$avg\n";
$m++;
}
close (FILE);
[download]

I am looking to change the array name dynamically... How this can be possible?

It's possible using a Perl feature called "symbolic references", but they are usually a very dangerous idea. So dangerous, in fact, that one of the effects of adding "use strict" to your program (and you should _always_ add "use strict" to your program) is to ban their use.

I know you think that this is the best solution to your problem, but it really isn't. There's always a better solution.

--
<http://dave.org.uk>

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg

Looking at this "more complete"(?) version of your code, it's actually easier for me to say how it can be done without trying to use "dynamic array names", and instead using an appropriate data structure (an array of arrays, or AoA). So I'll try to do that by showing how I would rewrite this.

But in trying to revise your code, I found a number of other problems, which will probably lead to unintended results. So, in addition to recasting the code to use an AoA, I made other changes to improve legibility: moved things around a bit, applied proper indentation (which does matter), used the simpler form of loop control, removed some unnecessary code, and removed your original comments.

Now, the only comments are the ones I put in, mostly (the "um..." ones) to mark things that make no sense or problems that need to be solved (but I don't know how you should solve them, because I don't know enough about your data or your real goals). This version compiles with no errors or warnings, but when you run it, there will certainly be a run-time error.

#!/usr/bin/perl -w

use strict;

my $dinu_r;  # um... nothing is ever assigned to this variable

my @energyGrid; # this will be the AoA

my $i;
for my $x ( 1 .. 5 )
{
    open( AA, "shuffle$x" ) or die "Can't open shuffle$x ($!)\n"; # LI
+NE A

    my $Sequence;
    $i=length($Sequence);  # um... this is always zero

    while (<AA>) {
        $Sequence=$_;  # um... $Sequence will only be the last line of
+ "shuffle$x"
    }
    close(AA);

    my %Winenergy = Energy( $Sequence, $dinu_r );
    open (OUT, ">shuffle$x.stb"); # LINE B

    foreach my $el1 (sort{$a <=> $b} keys %Winenergy) {
        push( @{$energyGrid[$x]} , $Winenergy{$el1} ); #LINE C
    }
    close (OUT);
}

open(FILE,">total_shuffle.stb");
my $m=8;

for my $j ( 0 .. $i )  # um... $i is still zero here
{
    my $avg = 0;
    for my $x ( 1 .. 5 ) {
        $avg += $energyGrid[$x][$j];
    }
    $avg /= 5;
    print FILE "$m\t$avg\n";
    $m++;
}
close (FILE);

sub Energy
{
    my ($sequence,$dinu_r) = @_;
    my %dinu = %$dinu_r;   # um... $dinu_r was never a hash ref
       # (and is undef), so this line will cause a run-time error

    my $win=15;
    my $limit1 = length( $sequence ) - $win + 1;
    my $wincenpos = 1 + ($win-1)/2;
    my %winenergy = ();
    for my $j ( 0 .. $limit1-1 ) {
        my $winseq = substr($sequence,$j,$win);
        my $energy = 0;
        for my $k  ( 0 .. $win-2 ) {
            my $dinucle_temp = substr($winseq,$k,2);
            my $dinucle = uc($dinucle_temp);
            $energy = $energy + $dinu{$dinucle};
        }
        my $wincentre = $j+$wincenpos;
        $winenergy{$wincentre} = $energy;
    }
    return %winenergy;
}
[download]

Hi graff!
Thanks for the effort you have put man. The things you have mentioned here, can not be taught by any book. I desperatly want to improve my Perl skills but that process is really slow as no experiance coder (monk :) ) is around.

I sincerely thank you and other monks who had taken time for my problem. One more thing, if I will be getting this kind of support, it wont be long that I will be helping some one out

Keep rocking monks!!