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

use 5.010;

##you will print results but first remove any previous files

my $cgs = "cg_size.txt";
if (unlink($cgs) == 1) {
           print "Existing \"cg_size.txt\" file was removed\n";
           }
                    
#now make a file for the core genome sizes output
           my $output_cgs = "cg_size.txt";
           
           if (! open(CGS, ">>$output_cgs") ) {
                      print "Cannot open file \"$output_cgs\" to write to!!\n\n";
                      exit;
                      }

my @tests = do {
   my $randomFile = q{random.txt};
   open my $randomFH, q{<}, $randomFile
      or die qq{open: < $randomFile: $!\n};
   map [ split ],
   <$randomFH>;
   };

my $columnFile = q{re-organized.txt};
open my $columnFH, q{<}, $columnFile
   or die qq{open: < $columnFile: $!\n};

my @results;
while ( <$columnFH> )
{
    my @cols = split;
    foreach my $idx ( 0 .. $#tests )
    {
	foreach my $subidx ( 0 .. $#{ $tests[ $idx ] } )
	{
	    my @posns = split m{,}, $tests[ $idx ]->[ $subidx ];
	    $results[ $idx ]->[ $subidx ] ++
	       if scalar @posns == grep { q{z} eq $cols[ $_ ] } @posns;
	}
    }
}

close $columnFH
   or die qq{close: < $columnFile: $!\n};

say CGS qq{@$_} for @results;