def tree():
"""Returns an annotated Bio.Phylo tree.
"""
with open("tests/data/flu_seasonal_h3n2_ha_3y_tree.json") as fh:
json_tree = json.load(fh)
tree = json_to_tree(json_tree)
return tree
def get_phylogeny(tree_path, tree_type="newick"):
if tree_type == "newick":
with open(tree_path) as f:
for phylogeny in Phylo.parse(f, "newick"):
break
return phylogeny
elif tree_type == "auspice_json":
with open(tree_path) as f:
tree = json.load(f)
phylogeny = json_to_tree(tree)
return phylogeny
else:
raise ValueError(f"current tree_type {tree_type} not supported")
help="tab-delimited file of attributes per node of the given tree")
parser.add_argument("--include-internal-nodes",
action="store_true",
help="include data from internal nodes in output")
parser.add_argument(
"--attributes",
nargs="+",
help="names of attributes to export from the given tree")
args = parser.parse_args()
# Load tree from JSON.
with open(args.tree, "r") as fh:
tree_json = json.load(fh)
tree = json_to_tree(tree_json)
# Collect attributes per node from the tree to export.
records = []
if args.attributes:
attributes = args.attributes
else:
attributes = sorted(
list(tree.root.node_attr.keys()) +
list(tree.root.branch_attrs.keys()))
for node in tree.find_clades(terminal=True):
if node.is_terminal() or args.include_internal_nodes:
record = {"name": node.name}
help="earliest date to show on the x-axis")
parser.add_argument("--end-date", help="latest date to show on the x-axis")
parser.add_argument(
"--include-color-bar",
action="store_true",
help=
"display a color bar for the color by option at the bottom of the plot"
)
args = parser.parse_args()
if args.tree.endswith(".json"):
with open(args.tree, "r") as json_fh:
json_tree = json.load(json_fh)
# Convert JSON tree layout to a Biopython Clade instance.
tree = json_to_tree(json_tree)
# Plot the tree.
plot_tree(tree, args.output, args.colorby, args.branch_width,
args.tip_size, args.start_date, args.end_date,
args.include_color_bar)
else:
tree = read_tree(args.tree)
tree.ladderize()
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
Bio.Phylo.draw(tree,
axes=ax,
label_func=lambda node: "",
show_confidence=False)
plt.savefig(args.output)