A mixed integer programming solution to the maximum phylogenetic diversity with cost constraints problem. Requires the following packages: docopt, scikit-bio, and pulp
Usage:
choose_optimal_leaves.py <tree> <costs> <budget> <num_leaves_to_choose> [-v -h -o]
Arguments:
<tree> Newick formatted tree that contains all the tips to be considered
<costs> Costs file with line of tip_name and cost separated by space
<budget> Total sum of costs to stay under
<num_leaves_to_choose> Number of active tips in final solution
Options:
-v --verbose Verbose logging
-h --help Help text
In the example subdir you will find a sample costs file (example_costs.txt) and a pruned phylogenetic tree that has the candidate cells (first column of costs file) as tips (example_phylogenetic_placement_subtree.txt). The third file (chosen_samples.txt) is the result of the following call:
python choose_optimal_leaves.py example/example_phylogenetic_placement_subtree.txt example/example_costs.txt 300 150 > example/chosen_samples.txt