#!/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
my $CountLines = 0; # total nr of lines in all files

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

  for ($j=1; $j<=2; $j++) {
    open $input2, '<', "$path\/File-${molec2}-cluster${j}.out" or die $!;
    push @ARGV, "$path\/File-${molec2}-cluster${j}.out";
}

    print "@ARGV \n"; # for testing; indeed correct files are printed

## now split and print

  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;
      print "@columns \n"; ## problem: prints all columns from specified files but ignores the $nextUnless specification - why?
    }

close $input1;
close $input2;

   for ($a=0; $a<=$#columns; $a++) {
      for ($b=0; $b<=$#columns; $b++) {
        print "$list[$a][$b] "; ## problem: prints only first file ($i=1) 
      }
      print " \n";
   }