#Handle the case of overlapping groups
$groupID = 1;
my %groupSeen;
foreach my $group1 (keys %groupOfBact){
	foreach my $group2 (keys %groupOfBact){
		if ($group1 != $group2){
			foreach my $strain (keys %{$groupOfBact{$group1}}){
				if((exists $groupOfBact{$group2}{$strain})&&(!exists $groupSeen{$strain})){
					%{$updatedGroupHash{$groupID}} = (%{$groupOfBact{$group1}}, %{$groupOfBact{$group2}});
					foreach my $seen (keys %{$updatedGroupHash{$groupID}} ){
						$groupSeen{$seen}=1;
					}
					$groupID++;
					last;
				}
				else {
					%{$updatedGroupHash{$groupID}} = %{$groupOfBact{$group1}};
				}
			}
		}
	}
}