F1-recombination.ipynb running error

[virologist]

Hi, there
I am trying to repeat the figure generated by F1-recombination.ipynb and generate my tangle tree by baltic. I met an error which indicates

def euclidean((x1,y1,x2,y2):
^
SyntaxError: invalid syntax

Here is the code I run. The baltic.py was obtained from the evogytis.

import imp
bt = imp.load_source('baltic', 'E:/Bio/Jupyter/baltic/baltic.py')
from glob import glob
from collections import defaultdict
import re
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
import matplotlib as mpl
import pickle
%matplotlib inline
import random
from pprint import pprint

treefiles = glob('E:/Bio/Jupyter/siv-cst/RAxML_bestTree*')
treefiles.sort(key=lambda x: int(x.split('_')[-2]))
def make_bt_tree(treefile):
t = bt.tree()
bt.make_tree(open(treefile, 'r').readlines()[0].strip(), t)
t.treeStats() ## initial traversal, checks for stats
t.sortBranches() ## traverses tree, sorts branches, draws tree
return t
trees = { i:make_bt_tree(treefile) for i,treefile in enumerate(treefiles)}

After this step, I got the same results as yours.

Tree height: 4.249024
Tree length: 27.026251
Numbers of objects in tree: 124 (61 nodes and 63 leaves)
...................

However, when I move to the next step I met this error. I didn't modify any code of this cell.

def euclidean((x1,y1),(x2,y2)):
return ((float(x2)-float(x1))**2+(float(y1)-float(y2))**2)**0.5
def sum_tip_distances(tree1,tree2):
tree1_tips = { k.numName: k for k in tree1.Objects if k.branchType=='leaf' }
tree2_tips = { k.numName: k for k in tree2.Objects if k.branchType=='leaf' }
shared_tips = set(tree1_tips.keys()).intersection(set(tree2_tips.keys()))
total_dist = 0.0
for t in shared_tips:
total_dist += euclidean( (tree1_tips[t].x, tree1_tips[t].y), (tree2_tips[t].x, tree2_tips[t].y) )
return total_dist
def untangle(tree1, tree2):
current_distance = sum_tip_distances(tree1, tree2)
for n in sorted(tree2.nodes,key=lambda x: -x.height):
if n.parent=='Root':
continue
n.rotate()
tree2.drawTree()
new_distance = sum_tip_distances(tree1, tree2)
if new_distance <= current_distance:
current_distance = new_distance
continue
else:
n.rotate()
tree2.drawTree()
for i in range(1,len(trees)):
untangle(trees[i-1], trees[i])

Could you please help me figure it out?
Thanks