def run_tests():
# initialization
import charmatrix
cm = charmatrix.charmatrix("data/data2.txt")
trees = list(all_trees(cm.taxon_set(), cm.get_outgroup()))
# test equality checking and construction
assert node(leaf(1), leaf(2)) == node(leaf(2), leaf(1)), "trees should be the same"
# test tree.size
assert trees[0].size() == 5, "there are 5 taxa in the tree"
# test all_trees
assert len(trees) == 15, "there are 15 trees for 4 taxa (excluding outgroup)"
assert len(set(trees)) == 15, "trees should be unique"
# test one_tree
assert one_tree(cm).taxon_set() == cm.taxon_set(), "taxa in one_tree should be those in charmatrix"
# test best and one_best
correct_tree = parse("(0,(1,(2,(3,4))))")
best_trees, length = best(trees, cm)
assert len(best_trees) == 1, "there is only one optimal tree"
assert best_trees[0] == correct_tree, "best tree is not correct"
assert length == 8, "length of best tree is 8"
one = one_best(trees, cm)
assert one == correct_tree, "one_best should also return this tree"
def main(args):
if args.test:
import run_tests
run_tests.run()
else:
cm = charmatrix.charmatrix(args.datafile)
cm.print_summary()
if args.algorithm == 'exhaustive':
import exhaustive
trees = exhaustive.exhaustive_search(cm)
for tree in trees:
print tree.to_string(cm)
elif args.algorithm in ('bnb', 'branch-and-bound'):
import branchnbound
trees = branchnbound.branchnbound_search(cm)
for tree in trees:
print tree.to_string(cm)
else:
import parallel_search
comm = parallel_search.communicator(cm, args.time, args.interval)
if args.algorithm == 'nni':
import nni
nni.nni_search(cm, comm)
elif args.algorithm == 'spr':
import spr
spr.spr_search(cm, comm)
elif args.algorithm == 'tbr':
import tbr
tbr.tbr_search(cm, comm)
elif args.algorithm == 'mixed':
import mixed
mixed.mixed_search(cm, comm)
def run_tests():
# random_not_in
my_set = set([1, 2, 3, 4])
assert random_not_in(5, my_set) == 0, "it can only be 0"
# random_in
assert random_in(5, my_set) in my_set, "number must be in set"
# list_tree itself
import charmatrix
# prepare trees
cm = charmatrix.charmatrix('data/shortoryzos.txt')
t = tree.one_tree(cm)
# test conversion with tree
lt = list_tree(tree=t)
tt = lt.to_tree()
assert tt == t, "list_tree <=> tree conversion should be reversible"
# test length
assert t.length(cm) == lt.length(cm), "tree length should give same result for tree and list_tree"
# test init_from_taxa
taxa = cm.taxon_set()
outgroup = cm.get_outgroup()
lt2 = list_tree(taxa=taxa, outgroup=outgroup)
assert lt2.to_tree().taxon_set() == taxa
def run_tests():
import charmatrix
cm = charmatrix.charmatrix("data/data2.txt")
t = exhaustive_search(cm)
assert t == tree.parse("(0,(1,(2,(3,4))))"), "exhaustive search must return this tree"
