def alternate_admixes(self, n=1000):
for i in xrange(n):
old_tree = deepcopy(self.tree)
self.tree = addadmix(
self.tree,
new_node_names=['n' + str(i) + a for a in ['o', 'n']])
if self.no_admixes + 1 == get_number_of_admixes(self.tree):
print 'INCREASED NUMBER OF ADMIXTURES BY ONE= ' + 'TRUE'
else:
print 'INCREASED NUMBER OF ADMIXTURES BY ONE= ' + 'FALSE'
ad = make_consistency_checks(self.tree, ['s1', 's2', 's3', 's4'])
if not ad[0]:
print ad
plot_graph(old_tree, drawing_name='good.png')
plot_graph(self.tree, drawing_name='bad.png')
break
#plot_graph(self.tree)
old_tree = deepcopy(self.tree)
self.tree = deladmix(self.tree)
if self.no_admixes == get_number_of_admixes(self.tree):
print 'DECREASED NUMBER OF ADMIXTURES BY ONE= ' + 'TRUE'
else:
print 'DECREASED NUMBER OF ADMIXTURES BY ONE= ' + 'FALSE'
#plot_graph(self.tree)
print self.tree
ad = make_consistency_checks(self.tree, ['s1', 's2', 's3', 's4'])
if not ad[0]:
print ad
plot_graph(old_tree, drawing_name='good.png')
plot_graph(self.tree, drawing_name='bad.png')
deladmix(old_tree)
break
def topological_support(start_tree, n=10000, nodes=None):
from tree_plotting import plot_as_directed_graph, plot_graph, pretty_print, pretty_string
tree = start_tree
score = 0
for i in range(n):
prop_index = choice(3, 1)
if prop_index == 0 and get_number_of_admixes(tree) > 0:
new_tree = deladmix(tree)[0]
score -= 1
elif prop_index == 1:
new_tree = make_regraft(tree, _get_new_nodes(i, prop_index))[0]
elif prop_index == 2:
new_tree = addadmix(tree, _get_new_nodes(i, prop_index))[0]
score += 1
else:
new_tree = tree
consistent, information = make_consistency_checks(new_tree, nodes)
if consistent:
if get_number_of_admixes(new_tree) < 50:
tree = new_tree
else:
print information
print 'last_good_tree', tree
print 'new_bad_tree', new_tree
plot_as_directed_graph(tree, drawing_name='before.png')
wait(1)
plot_as_directed_graph(new_tree, drawing_name='after.png')
wait(1)
if i % 1000 == 0:
plot_as_directed_graph(tree,
drawing_name='number_' + str(i) + 'K.png')
wait(1)
plot_as_directed_graph(tree, drawing_name='final_tree.png')
wait(1)
return score
def check(tree, pks={}):
result, fails = make_consistency_checks(tree)
if not result:
stringed_message = ''
print fails
for test_key, (test_result, test_message) in fails.items():
if test_result:
stringed_message += test_key + ": TRUE" + '\n'
else:
stringed_message += test_key + ": FALSE" + '\n'
stringed_message += " " + test_message + '\n'
print stringed_message
assert result, "The tree was inconsistent :" + '\n' + stringed_message
def many_admixes(self, n=100):
for i in xrange(n):
self.tree = addadmix(
self.tree,
new_node_names=['n' + str(i) + a for a in ['o', 'n']])
#plot_graph(self.tree)
if self.no_admixes + 1 == get_number_of_admixes(self.tree):
print 'INCREASED NUMBER OF ADMIXTURES BY ONE= ' + 'TRUE'
else:
print 'INCREASED NUMBER OF ADMIXTURES BY ONE= ' + 'FALSE'
self.no_admixes = get_number_of_admixes(self.tree)
ad = make_consistency_checks(self.tree, ['s1', 's2', 's3', 's4'])
if not ad[0]:
print ad
plot_graph(self.tree, drawing_name='bad.png')
break
plot_as_directed_graph(self.tree)