print Dumper \@list; # check that the content of @list is what you exp
+ect
[download]

Sorry I should have said that in the last nested for loop I am *for now* only printing for testing. This is where all the maths will be which is all written in a  $list[$a][$b] basis, I'm just printing here for testing. The rest of the code works, It's just that i now need to make it work for a combination of multiple files, rather than on couples of files like I did so far. That's why Dumper \@list isn't suitable.

Basically what I want to know is: is there a way to open those files with two for loops like so

for ($i; $i<=4; $i++) {
  for ($j; $j<=4; $j++) {

#etc

while <lines_of_both_$i_and_$j_files> {

#etc
[download]

This was why I tried to use while <>: extensive googling told me that using @ARGV and the diamond operator was the most efficient way to open multiple files and read them line by line with while. I have a perfectly working script that does all the maths I need but unfortunately it's only doing it for while <$line>. How do I tell perl that I want this done for while <lines_of_both_$i_and_$j_files>? I guess that's what my question boils down to.

I'm sorry I'm really struggling with this, getting really stressed and frustrated that I'm constantly buggering it up and can't even explain properly. I am very grateful for all contributions here and I'm reading and studying all of them, however not understanding everything. Quite disheartening as I've been "coding" on and off for a couple years now so expected to have learnt more

With multiple files then maybe what you want is a 3 dimensional array ?

#!/bin/perl/
use strict;
use warnings;

my $molec1 = "molec1";
my $molec2 = "molec2";

my $path = "/store/group/comparisons";
my @matrix;
my @files;

for my $i (1..3){
  push @files, $path."/File-$molec1-cluster$i.out"
}

for my $j (1..2){
  push @files, $path."/File-$molec2-cluster$j.out"
}

my @all = ();
for my $filename (@files){
  open my $fh,'<',$filename or die "Could not open $filename";
  my @matrix = ();
  while (my $line = <$fh>){
    next if ($line  =~ /^#/);
    chomp $line;
    push @matrix,[split /\s+/,$line];
  }
  close $fh;
  push @all,\@matrix;
}

my $matrices = scalar @all;
for my $i (0..$matrices-1){
  print $files[$i]."\n";
  my $rows = scalar @{$all[$i]};
  for my $r (0..$rows-1){
    my $cols = scalar @{$all[$i][$r]};
    for my $c (0..$cols-1){
      print "$all[$i][$r][$c] "
    }
    print "\n";
  }
  print "\n";
}
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poj

Basically what I want to know is: is there a way to open those files with two for loops like so

for ($i; $i<=4; $i++) {
  for ($j; $j<=4; $j++) {

#etc
[download]

Yes, you can do that, but that would be very inefficient and that's most probably not what you should do, because it would mean opening the second series of files a number of times, and there is nothing in what you've described that would make this necessary.

With the code that I have provided in my first post (including the small corrections I made on the @ARGV array that I had forgot to remove in the second for loop), you should be able to read all the files.

If, on the other hand, you want to combine in some ways files from your first set with files of your second set, then it is more complicated, but you still don't want to read the same files many times over. But the bottom line is that there is nothing in what you said so far that indicates something in this direction.

As an aside, fasoli, you said,

... perform some mathematical calculations on the combination of matrices ... I haven't included this bit of the code yet but (fingers crossed) it works.

When Marshall posted his example matrix_transpose, I was reminded that I wanted to point out: instead of crossing your fingers that your (or Marshall's) roll-your-own-code truly works, there are plenty of modules and families of modules that will do the matrix math and have been fully tested across edge cases. Math::MatrixReal, Math::GSL, and PDL::Matrix are three such well-tested Matrix modules. It is probably worth your time to try out one or more of those -- their math has been checked thoroughly over the years, and they are likely to run faster (Benchmark), too.

Probably the best-performing one would be the LAPACK-wrapper, PDL::LinearAlgebra - it has nice wrappers for LAPACK, or if you prefer, you can access the raw LAPACK functions.