def small_parsimony_unrooted(Tree, leaves):
T = copy.deepcopy(Tree)
nodes = T.keys()
root = len(nodes)
'''take the last node as default the maximal node num, add root to it'''
nodei = len(nodes) - 1
nodej = max(T[len(nodes) - 1])
T[nodei].remove(nodej)
T[nodej].remove(nodei)
T[root].append(nodei)
T[root].append(nodej)
T[nodei].append(root)
T[nodej].append(root)
cols = zip(*leaves.values())
ret = []
scores = 0
n = len(leaves)
for i in range(len(leaves[0])):
Character = dict(zip(range(n), cols[i]))
score, col = sp.small_parsimony(T, Character)
ret.append(col.values())
scores += score
finalCharacter = dict(zip(T.keys(), zip(*ret)))
result = printTree(T, finalCharacter, scores)
return result, finalCharacter
def small_parsimony_unrooted(Tree,leaves): T = copy.deepcopy(Tree) nodes = T.keys() root = len(nodes) '''take the last node as default the maximal node num, add root to it''' nodei = len(nodes)-1 nodej = max(T[len(nodes)-1]) T[nodei].remove(nodej) T[nodej].remove(nodei) T[root].append(nodei) T[root].append(nodej) T[nodei].append(root) T[nodej].append(root) cols = zip(*leaves.values()) ret = [] scores = 0 n = len(leaves) for i in range(len(leaves[0])): Character = dict(zip(range(n),cols[i])) score,col = sp.small_parsimony(T,Character) ret.append(col.values()) scores += score finalCharacter = dict(zip(T.keys(),zip(*ret))) result = printTree(T,finalCharacter,scores) return result,finalCharacter
def printTree(T, Character, scores):
print_ret = []
finalCharacter = {}
source = max(T.keys())
distTo, edgeTo = sp.bfs(T, source)
nodes = sorted(T.keys(), reverse=True)
nodei = T[source][0]
nodej = T[source][1]
str0 = ''.join(Character[source])
str1 = ''.join(Character[nodei])
str2 = ''.join(Character[nodej])
scores -= sp.hamming_distance(str0, str1)
scores -= sp.hamming_distance(str0, str2)
scores += sp.hamming_distance(str1, str2)
print_ret.append(str(scores))
for node in nodes:
if node == source:
continue
finalCharacter[node] = ''.join(Character[node])
path = sp.pathTo(node, distTo, edgeTo)
parent = path[1]
if parent == source:
continue
str1 = ''.join(Character[node])
str2 = ''.join(Character[parent])
print_ret.append(str1 + '->' + str2 + ':' +
str(sp.hamming_distance(str1, str2)))
print_ret.append(str2 + '->' + str1 + ':' +
str(sp.hamming_distance(str1, str2)))
nodei = T[source][0]
nodej = T[source][1]
str0 = ''.join(Character[source])
str1 = ''.join(Character[nodei])
str2 = ''.join(Character[nodej])
print_ret.append(str1 + '->' + str2 + ':' +
str(sp.hamming_distance(str1, str2)))
print_ret.append(str2 + '->' + str1 + ':' +
str(sp.hamming_distance(str1, str2)))
return print_ret
def printTree(T,Character,scores):
print_ret = []
finalCharacter = {}
source = max(T.keys())
distTo,edgeTo = sp.bfs(T,source)
nodes = sorted(T.keys(),reverse=True)
nodei = T[source][0]
nodej = T[source][1]
str0 = ''.join(Character[source])
str1 = ''.join(Character[nodei])
str2 = ''.join(Character[nodej])
scores -= sp.hamming_distance(str0,str1)
scores -= sp.hamming_distance(str0,str2)
scores += sp.hamming_distance(str1,str2)
print_ret.append(str(scores))
for node in nodes:
if node == source:
continue
finalCharacter[node] = ''.join(Character[node])
path = sp.pathTo(node,distTo,edgeTo)
parent = path[1]
if parent == source:
continue
str1 = ''.join(Character[node])
str2 = ''.join(Character[parent])
print_ret.append(str1+'->'+str2+':'+str(sp.hamming_distance(str1,str2)))
print_ret.append(str2+'->'+str1+':'+str(sp.hamming_distance(str1,str2)))
nodei = T[source][0]
nodej = T[source][1]
str0 = ''.join(Character[source])
str1 = ''.join(Character[nodei])
str2 = ''.join(Character[nodej])
print_ret.append(str1+'->'+str2+':'+str(sp.hamming_distance(str1,str2)))
print_ret.append(str2+'->'+str1+':'+str(sp.hamming_distance(str1,str2)))
return print_ret
