#!/bin/perl/

use strict;
use warnings;

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

my $input1;
my $input2;

@ARGV = ();

my $i;
my $j;

my $path = "/store/group/comparisons";

my $line;
my @columns;

my $nextUnless = 2; # nr of lines to skip from beginning
my $CountLines = 0; # total nr of lines in all files, including comments

for ($i=1; $i<=3; $i++) {
  open $input1, '<', "$path\/File-${molec1}-cluster${i}.out" or die $!;
  for ($j=1; $j<=4; $j++) {
    open $input2, '<', "$path\/File-${molec2}-cluster${j}.out" or die $!;

  push @ARGV, $input1;
  push @ARGV, $input2;

  my @list;
  my $list;
  my $a;
  my $b;

     while ($line = <>) {
       $CountLines += 1;
       next unless $. > $nextUnless;
       chomp $line;
       $line =~ s/^\s+|\s+$//g;
       push @list, [split/\s+/, $line];
       @columns = split /\s+/, $line;
     }

  close $input1;
  close $input2;

     for ($a=0; $a<=$#columns; $a++) {
       for ($b=0; $b<=$#columns; $b++) {
         print "$list[$a][$b] "; # to check matrices
       }
     print " \n";
    }
  } # for j
} # for i