Hi again all. Thanks to your help I solved my first problem, thank you again. I'm after some feedback about a second problem I'm facing.

So, first I'm opening four files that each have one 3x3 matrix in them, that looks like this

1  2  3
4  5  6
7  8  9
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2  3  4
4  5  6
7  8  9
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1  2  3
4  5  6
7  8  9
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3  4  5
4  5  6
7  8  9
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Now I want to do some basic math on the elements of the matrices, namely to get their average value (and then proceed to get the standard deviation, I haven't tried that yet). As I said they are four 3x3 test matrices, each one in a different file. These are test cases as my real matrices are thousands of lines long and the number of files is again thousands. So I'm after a new matrix that will have the average values of the four matrices, like so (first line only) - obviously the new matrix elements are filled with the sum of the elements divided by the number of the matrices, for example for the first line 1 + 2 + 1 + 3 = 7 / 4 = 1.75. Then the second element, 2 + 3 + 2 + 4 = 11 / 4 = 2.75. And the third element of the first line 3 + 4 + 3 + 5 = 15 / 4 = 3.75 and so on for all the elements, resulting in one matrix.

1.75  2.75  3.75
 x      x     x
 x      x     x
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When I print the matrices with $line[$a][$b] they look correct, so I've commented this line out as it was used as a test to see if they look ok. The output I'm getting if I try to get the sum of the elements and then the mean, is Use of uninitialized value in addition (+) at test_SD_Wednesday.pl line 52 and a bunch of wrong numbers as sum/averages. I'm pretty sure I'm screwing something up badly but I can't figure out what. Any hints please? I'm starting to get scared my supervisors will really shout at me or think I'm an idiot if I tell them it's taken me 10 days to have a script that doesn't work...

Finally can someone comment on the indentation? Does it make sense they way I did it? It looks less messy but no clue if I got the philosophy behind it.

#/bin/perl/

use strict;
use warnings;
use autodie;

my $molec = "1ac6";
my $cluster;
my $times;
my $input;

my $path = "/media/RAIDstorage/home/athina/dist-analysis/${molec}/time
+series/test";

my $line;
my @files;
@files = `ls $path\/$molec-times*`;

foreach (@files) {

 my $a;
 my $b;

 my $m_avrg;

 my @m_avrg;
 undef @m_avrg;

 my @list;
 my $list;

 my $aver;

 /${molec}-times-(\d+)-clust(\d{1})/;

 $times = $1;
 $cluster = $2;

 open $input, '<', "$path\/${molec}-times-${times}-clust${cluster}.out
+" or die $!;

 while ($line = <$input>) {
  chomp $line;

  push @list, [split/\s+/, $line];

 } # while input

 close $input;

  for ($a=0; $a<=2; $a++) {
   for ($b=0; $b<=2; $b++) {
    #print "$list[$a][$b] "; # check matrices
    $m_avrg[$a][$b] = ($m_avrg[$a][$b] + $list[$a][$b]);
    print  "$m_avrg[$a][$b] \n";
   }
   print " \n";
  }

   print "average\n";
    
   for ($a=0; $a<=2; $a++) {
    for ($b=0; $b<=2; $b++) {
     $m_avrg[$a][$b] = $m_avrg[$a][$b] / 4;
     print "$m_avrg[$a][$b] ";
     }
    print "\n";
   }

} # foreach file in loop
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