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;
}

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In reply to Re^3: Changing name of ARRAY in each iteration by graff
in thread Changing name of ARRAY in each iteration by cool

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