def main(tree_fn):
if not os.path.exists(tree_fn):
print("Input tree file does not exist: %s" % tree_fn)
t = tree.Tree(tree_fn, format=1)
CheckTree(t)
d = AveDist(t)
print("Average distance from root to leaves: %f" % d)
for n in t.traverse('preorder'):
if n.is_root():
n.dist = 0
continue
# work downwards, setting the branch distances from the top down
x = t.get_distance(n) - n.dist
y = n.dist
print("\nTaxa:")
print(", ".join(n.get_leaf_names()))
if n.is_leaf():
z = 0.
else:
z = AveDist(n)
print("Distance of parent node from root: %f" % x)
print("Current branch length: %f" % y)
print("Average distance to leaves: %f" % z)
if (y+z) == 0.:
n.dist = 0
else:
f = (d-x)/(y + z)
n.dist = f * n.dist
print("Branch length for ultrametric tree: %f" % n.dist)
outfn = tree_fn + ".ultrametric.tre"
t.write(outfile=outfn, format=5)
print("\nUltrametric tree written to: %s\n" % outfn)
def ReplaceFileWithNewIDs(idsMap, treeFilename, newTreeFilename):
t = tree.Tree(treeFilename, format=1)
for node in t.get_leaves():
node.name = idsMap[node.name]
outputTreeString = t.write(format=1)
with open(newTreeFilename, 'wb') as outFile:
outFile.write(outputTreeString)
def ReplaceFileWithNewIDs(idsMap, treeFilename, newTreeFilename):
qHaveSupport = False
qHaveInternalNames = False
try:
t = tree.Tree(treeFilename, format=2)
qHaveSupport = True
except:
try:
t = tree.Tree(treeFilename, format=3)
qHaveInternalNames = True
except:
t = tree.Tree(treeFilename)
for node in t.get_leaves():
node.name = idsMap[node.name]
if qHaveSupport:
t.write(outfile=newTreeFilename)
elif qHaveInternalNames:
t.write(outfile=newTreeFilename, format=3)
else:
t.write(outfile=newTreeFilename, format=5)