tree=base_name + ".nwk",
aln=base_name + '.fasta',
verbose=0)
# infer a GTR model and ML ancestral sequences, either marginally or jointly most likely
myTree.infer_ancestral_sequences(infer_gtr=True, marginal=True)
# lets examine the properties of a node in the tree after ancestral inference
node = myTree.tree.get_nonterminals()[7]
# each node now has an inferred sequence
if treetime.version < "0.7":
print("\nthe inferred sequences is an array of characters:",
node.sequence)
else:
print("\nthe inferred sequences is an array of characters:",
myTree.sequence(node, as_string=False))
# in addition, each node of the tree now has an mutation object attached
# note that the mutation numbering starts at 0 rather than 1
print("\nmutations on the branch leading to node %s:" % node.name,
node.mutations)
# we can readily verify these mutations by checking the inferred sequences
if node.mutations:
mut = node.mutations[0]
if treetime.version < "0.7":
print(
"\nmutation %s%d%s corresponds to" % mut,
"parent state: %s, child state %s\n\n" %
(node.up.sequence[mut[1]], node.sequence[mut[1]]))
else:
print("the following features are in the supplied as genes but not the annotation:", set(args.genes).difference(features.keys()))
T = Phylo.read(args.tree, 'newick')
leafs = {n.name for n in T.get_terminals()}
node_data = {}
root_sequence_translations = {}
for gene, translation in zip(genes, translations):
seqs = []
for s in SeqIO.parse(translation, 'fasta'):
if s.id in leafs:
seqs.append(s)
tt = TreeAnc(tree=T, aln=MultipleSeqAlignment(seqs), alphabet='aa')
tt.infer_ancestral_sequences(reconstruct_tip_states=True)
root_sequence_translations[gene] = tt.sequence(tt.tree.root, as_string=True, reconstructed=True)
with open(translation.replace('.fasta', '_withInternalNodes.fasta'), 'w') as fh:
for n in tt.tree.find_clades():
if n.name not in node_data:
node_data[n.name] = {"aa_muts":{}}
if len(n.mutations):
node_data[n.name]["aa_muts"][gene] = [f"{a}{p+1}{d}" for a,p,d in n.mutations]
fh.write(f">{n.name}\n{tt.sequence(n, as_string=True, reconstructed=True)}\n")
annotations = annotation_json(features, ref)
with open(args.output, 'w') as fh:
json.dump({"nodes":node_data, "annotations":annotations, "reference":root_sequence_translations}, fh)