Hi everyone, I'm working on a bacterial neighbor grouping problem. Basically the idea is there are many strains of a particular type of bacteria and we are looking at grouping 'sets' of these together based on relatedness (i.e. Bacteria_1 is more closely related to Bacteria_2 than Bacteria_3 because 1 and 2 have many more genes in common than 3). I have gotten to the point where I have 2d hashes representing all the groups I've found. However some of these groups overlap, for example:

%groupOfBact

looks like:

group1=>(

strain1=>1,
strain2=>1,
strain4=>1

)

group2=>(

strain3=>1,
strain4=>1,
strain5=>1

)

group3=>(

strain6=>1,
strain7=>1

)

I would like to take %groupOfBact and merge the groups with common strains, while leaving the ones with no common strains intact. So, after the operation %groupOfBact would look like

group1=>(

strain1=>1,
strain2=>1,
strain3=>1,
strain4=>1,
strain5=>1

)

group2=>(

strain6=>1,
strain7=>1

)

I don't really care about what the values are afterwords (i.e. strain6=>10000 for all I care) and I think I have a structure that kind of works... but I feel like its really clunky, and even worse almost impossible for other people to read and understand. hrm, here's what it looks like:

#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{$groupI
+D}} ){
                        $groupSeen{$seen}=1;
                    }
                    $groupID++;
                    last;
                }
                else {
                    %{$updatedGroupHash{$groupID}} = %{$groupOfBact{$g
+roup1}};
                }
            }
        }
    }
}
[download]

Any help would be greatly appreciated! Oh, I've also taken a look at Hash::Merge, but it seems to break with some message about odd numbers of elements... I could be using it incorrectly however (I'm still pretty new to perl)

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