I am using a nested loop b/c I have external number of things that need to happen, then an internal number of things that corresponds directly to the external, then a super internal set of things that needs to correspond directly to the internal things.

i.e. MotherA -> ChildA -> genes within childA; MotherA -> ChildB -> genes within childB; MotherB -> ChildB -> genes within childB

I have a list of mothers and fathers that I am randomly combining by saying: 30 mothers (external) have "n" children (internal) from "n" fathers. The children then get n genes from father and n genes from mother (super internal).

I have a code that works exactly as I would like it to. However, the problem is when the number of mothers, and/or number of offspring per mother (think plants), and/or the number of genes I am tracking gets exceedingly large the run time of the script gets horrendously long. Here is a mock up of the code: 

 
use strict;
use warnings;

my $num_of_external = 30; #num moms

my @num_of_internal =  (30, 40, 20, 30, 40, 30, 40, 
                        20, 30, 40, 30, 40, 20, 30, 
                        40, 30, 40, 20, 30, 40, 30, 
                        40, 20, 30, 40, 30, 40, 20, 
                        30, 40); #num offspring per mom

my $num_of_super_internal = 10; #num genes tracked
#during shuffle 5 come from dad 5 come from mom

for (1 .. $num_of_external) {
    my $internal = shift @num_of_internal;
    
    #additional things here. 
    #i.e. select mother from possible pool

    for (1 .. $internal) {

        #select father for each offspring

        #additional things here.

        for (1 .. $num_of_super_internal) {
        
            #additional things here.
      #select genes and shuffle around between mom and dad.

        }
    }
}

[download]
Having gotten this far on my own, I am not sure how to avoid/do away with/restructure/alter/fix this nested loop structure. Is there any way to increase run time by changing the way I am thinking about loops?

Anything you monks can offer would be greatly appreciated by my overheating processor.

Bio

---- Even a blind squirrel finds a nut sometimes.

In reply to Nested loops of doom by BioNrd

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