def pd(tree, tips):
traveled = set()
traveled.add(tree_utils.get_mrca(list(tips), tree))
measure = 0
for i in tips:
c = i
while c not in traveled:
measure += c.length
if c.parent == None: #root
break
traveled.add(c)
c = c.parent
return measure
def phylo_dist(tip1,tip2,tree):
mrca = tree_utils.get_mrca([tip1,tip2],tree)
d1 = 0
d2 = 0
cn = tip1
while cn != mrca:
d1 += cn.length
cn = cn.parent
cn = tip2
while cn != mrca:
d2 += cn.length
cn = cn.parent
return d1+d2
print >> sys.stderr, "not matched", i.label
continue
done = set()
dates = {} # key is node, value is date
dates_names = {} #key is node, value is mrca string
for i in dated.iternodes(order="preorder"):
if len(i.children) == 0:
continue
else:
nds = []
for j in i.leaves():
if "node" in j.data:
nds.append(j.data["node"])
if len(nds) > 1:
x = tree_utils.get_mrca(nds, ott)
if x in done:
continue
done.add(x)
dates[x] = i.height
dates_names[x] = x.children[0].leaves(
)[0].label + "," + x.children[1].leaves()[0].label
# check backwards
dele = set()
for i in dates:
if i in dele:
continue
cur = i
while cur != None:
try:
if i.name not in removetaxa:
tr.write(i.get_fasta())
tr.close()
tree = tree_reader.read_tree_file_iter(sys.argv[2]).next()
nodes = {}
mrca_pars = [] #vector of the parents of each remove constraint
child_constraints = [
] #vector of child_constraints for each remove constraint
for i in tree.leaves():
nodes[i.label] = i
for i in remove_mrca:
tnods = []
for j in i:
tnods.append(nodes[j])
mr = tree_utils.get_mrca(tnods, tree)
par = mr.parent
tchild_constraints = []
for j in mr.children:
if len(j.children) > 0:
tchild_constraints.append(j)
j.parent = par
par.add_child(j)
child_constraints.append(tchild_constraints)
par.remove_child(mr)
mrca_pars.append(par)
for i in removetaxa:
# in case you remove
if i not in nodes:
continue
par = nodes[i].parent
mrca_checks[spls[0]].append(i)
except:
mrca_checks[spls[0]] = []
mrca_checks[spls[0]].append(i)
of = open(sys.argv[2], "r")
for i in of:
nm = i.strip()
nm1 = nm.split("_")[0]
if nm1 in mrca_checks:
print nm1, mrca_checks[nm1]
x = None
if len(mrca_checks[nm1]) == 1:
x = mrca_checks[nm1][0]
else:
x = tree_utils.get_mrca(mrca_checks[nm1], tree)
print x.get_newick_repr()
n2 = node.Node()
n2.label = nm
# is a tip
if len(x.children) == 0:
p = x.parent
# add a child
n = node.Node()
n.length = x.length / 2.
x.length = n.length
p.remove_child(x)
n.add_child(x)
n2.length = x.length
n.add_child(n2)
p.add_child(n)