def do_search(self, comm, trees=None): cm = self.cm if trees == None: first_tree = [tree.one_tree(cm)] first_len = first_tree[0].length(cm) print "Initial tree length: %d" % first_len else: first_tree = trees first_len = trees[0].length(cm) while not comm.need_to_communicate(): # preserve outgroup t = first_tree[0] new_tree = tree.node(t.left, rearrange_tree(t.right)) new_len = new_tree.length(cm) if new_len < first_len: print "New length, current minimum length: %d, %d" % (new_len, first_len) first_len = new_len first_tree = [new_tree] elif new_len == first_len: first_tree.append(new_tree) random.shuffle(first_tree) # commmunicate back return first_tree
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 initial_tree(self): return tree.one_tree(cm)