def calc_mcc_tree(tree_path, burnin):
treeannotater_cmd = 'treeannotator -burnin {0} {1} {2}'.format(
burnin, tree_path, tree_path.replace('.trees', '_mcc.tre'))
subprocess.run(shlex.split(treeannotater_cmd))
myTree = bt.loadNexus(tree_path.replace('.trees', '_mcc.tre'),
absoluteTime=False)
max_time = max([
float(item.name.split('_')[1]) for item in myTree.Objects
if item.branchType == 'leaf'
])
myTree.setAbsoluteTime(max_time)
return (myTree)
def test_beast2_traits(self):
print('Testing BEAST v2 trait parsing')
ll=bt.loadNexus('./tests/data/MERS.mcc.tree')
ll.traverse_tree()
print('Test if branches have correct number of traits')
assert len(ll.root.traits)==10
print('Root has correct number of traits')
for k in ll.Objects:
if k.is_node() and k!=ll.root:
assert len(k.traits)==13
elif k.is_leaf():
assert len(k.traits) in [9,12]
print('Branches have correct number of traits')
def test_beast1_traits(self):
print('Testing BEAST v1 trait parsing')
ll=bt.loadNexus('./tests/data/miniFluB.mcc.tree',tip_regex='_([0-9-]+)')
ll.traverse_tree()
print('Test if branches have correct number of traits')
assert len(ll.root.traits)==77
print('Root has correct number of traits')
for k in ll.Objects:
if k.is_node() and k!=ll.root:
assert len(k.traits) in [77,74,71,41]
elif k.is_leaf():
assert len(k.traits) in [76,73,70]
print('Branches have correct number of traits')
except ImportError:
from io import StringIO as sio
from io import BytesIO as csio
import requests
from Bio import Phylo
path = ##pathway to json file
treepath = ##pathway to mcc tree
# treeFile = 'aligned.tree'
# bstree = Phylo.read(path + treeFile, 'newick')
nx_tree = json.load(open(path + '/finalproject_filename.json','r'))
# do mcc stuff
ll = bt.loadNexus(treepath + '/file_mcc.tree')
tree = nx_tree['tree'] # tree data
meta = nx_tree['meta'] # metadata
# print(tree)
traitName = 'country_exposure' # trait used for colouring the tree
xspan = (0, 0.003)
typeface = 'Times New Roman'
mpl.rcParams['font.weight'] = 300
mpl.rcParams['axes.labelweight'] = 300
mpl.rcParams['font.family'] = typeface
mpl.rcParams['font.size'] = 12
from matplotlib.gridspec import GridSpec
#import requests
from io import StringIO as sio
from io import BytesIO as csio
# Can add more tree files for additional genome segments
fig_name = 'CoVSequentialTanglegram.png'
tree_file = "sars-like-CoVs-sub_"
segments=['1-2936','2937-4936','4937-6870','6871-8473','8474-19706','19707-20428']
"Load trees into tree dict"
trees={} ## dict
for segment in segments:
print(segment,)
treeFile = tree_file + segment + ".nexus"
ll=bt.loadNexus(treeFile,absoluteTime=False)
ll.setAbsoluteTime(2020.0)
trees[segment]=ll
print('\nDone!')
"Rescale tree heights so they are all equal"
tree_heights = []
for t,tr in enumerate(trees.keys()): ## iterate over trees
cur_tree=trees[tr] ## fetch tree object
tree_heights.append(cur_tree.treeHeight)
max_height_cap = max(tree_heights)
for t,tr in enumerate(trees.keys()): ## iterate over trees
cur_tree=trees[tr] ## fetch tree object
for k in cur_tree.Objects: ## iterate over a flat list of branches
k.length = k.length * (max_height_cap/cur_tree.treeHeight)
#print(k.height)
def test_nexus(self):
tree = bt.loadNexus('./tests/data/2020-04-13_treetime/divergence_tree.nexus')
tree.treeStats()
pass