slyalina / optimize_over_tree

A mixed integer programming solution to the maximum phylogenetic diversity problem

optimize_over_tree

A mixed integer programming solution to the maximum phylogenetic diversity with cost constraints problem. Requires the following packages: docopt, scikit-bio, and pulp

Invocation

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

Example

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