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 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)
def plot_string_tree(stree):
plot_graph(identifier_to_tree_clean(stree))
updat = updater(sigma / sqrt(2 * n - 2 + 4 * k))
new_tree = update_all_branches(new_tree, updat)
if new_tree is None:
return tree, 1, 0 #rejecting by setting backward jump probability to 0.
return new_tree, 1, 1
class rescale_class(object):
new_nodes = 0
proposal_name = 'rescale'
adaption = True
input = 'tree'
require_admixture = 0
reverse_require_admixture = 0
reverse = 'rescale'
admixture_change = 0
def __call__(self, *args, **kwargs):
return rescale(*args, **kwargs)
if __name__ == '__main__':
from tree_plotting import plot_graph
from Rcatalogue_of_trees import tree_on_the_border2_with_children
plot_graph(tree_on_the_border2_with_children)
new_tree = rescale(tree_on_the_border2_with_children)
plot_graph(new_tree)
print 'old_tree', tree_on_the_border2_with_children
print 'new_tree', new_tree
