def graph2tree(G, root=0, names=[]):
# assum G is acyclic
seed_node = Node()
seed_node.label = names[root] if names else str(root)
T = Tree(seed_node=seed_node)
n = len(G)
node_refs = [None for i in range(n)]
node_refs[root] = seed_node
count = 1
curr_v = root
stk = [root]
while len(stk) > 0:
curr_v = stk.pop()
for v, length in G[curr_v]:
if node_refs[v] is None:
stk.append(v)
new_node = Node()
new_node.label = names[v] if names else str(v)
node_refs[v] = new_node
node_refs[curr_v].add_child(new_node)
new_node.edge_length = length
for node in T.leaf_node_iter():
node.taxon = T.taxon_namespace.new_taxon(label=node.label)
return T
phylum] != node.nleaf:
#if phylum not in convergence or c.phylCount[phylum] > convergence[phylum][0]:
if phylum not in groupings:
groupings[phylum] = set([c])
else:
groupings[phylum].add(c)
#for phylum in global_phylCount:
# if global_phylCount[phylum] > 1 and not ('Candi' in phylum or 'candi' in phylum):
# print(phylum + " " + str(global_phylCount[phylum]) + " " + str(purity[phylum][0]) + " " + str(convergence[phylum][0]))
# print(phylum,global_phylCount[phylum])
#print(global_phylCount['Firmicutes'])
#print(purity['Firmicutes'])
for phylum in groupings:
if global_phylCount[phylum] < 2:
continue
if len(list(groupings[phylum])) == 1:
ID = None
else:
ID = 1
for c in groupings[phylum]:
#print(phylum + " " + c.label)
subTree = Tree(seed_node=c)
suffix = ("_" + str(ID)) if ID else ''
for node in subTree.leaf_node_iter():
print(node.taxon.label + " " + phylum + suffix)
if ID:
ID += 1