#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

# read in data

my $g_arr = [ ];
my $value_arr = [ ];

while ( <DATA> ) {
  chomp;

  # Assumes 2 genes per line in the first and second position!
  my @line = split /,/, $_, 3; 

  $line[2] =~ s/\s*$//;

  my $cluster_idx = 0;
  my @found = ( -1, -1 );
  foreach my $cluster ( @$g_arr ) {
    foreach my $poss_g_match ( @$cluster ) {
      if ( $line[0] eq $poss_g_match ) {
        $found[0] = 1;
      }
      if ( $line[1] eq $poss_g_match ) {
        $found[1] = 1;
      }
    }
    last if ( $found[0] != -1 || $found[1] != -1 );
    $cluster_idx++;
  }

  if ( $found[0] == -1 ) {
    push @{$g_arr->[$cluster_idx]}, $line[0];
  }
  if ( $found[1] == -1 ) {
    push @{$g_arr->[$cluster_idx]}, $line[1];
  }

  push @{$value_arr->[$cluster_idx]}, $line[2];
}

my $traversal_idx = 0;

foreach my $cluster ( @$g_arr ) {
  print join( ',', @$cluster) . " : " . join( ',', @{$value_arr->[$traversal_idx++]} ), "\n";
}

__DATA__
Gene1,Gene2,spc1,spc2
Gene3,Gene1,spc1,spc2,spc4
Gene4,Gene1,spc1,spc2,spc5,spc3,spc1
Gene2,Gene3,spc1,spc2
Gene2,Gene4,spc2,spc3
Gene3,Gene4,spc1,spc2
GeneA,GeneB,spc4,spc5
GeneB,GeneC,spc1,spc2
GeneC,GeneD,spc1,spc2
GeneD,GeneE,spc4,spc2
GeneE,GeneF,spc3,spc1
GeneX,GeneY,spc6,spc8
GeneX,GeneP,spc6,spc7
GeneUnknown.,GeneUnknown.,spc1,spc2