def parse_tree(t):
"""Simple function to read a tree file off the disk and return it as a
Tree object. Also calls the render() method on it so that it gets node IDs
that we can use to apply labels/marks."""
treeobj = EvolTree(t)
treeobj.render('')
return treeobj
def run_evol_py(tree,
alg,
branch_model,
site_models,
workir='data/evol_output',
tool_dir="ete3_apps/bin"):
print(tree, alg, branch_model, site_models)
builtin_apps_path = None
builtin_apps_path = os.path.join(os.path.split(ete3_path)[0], tool_dir)
tree = EvolTree(tree, binpath=builtin_apps_path)
tree.link_to_alignment(alg)
tree.workdir = workir
###branch model
if branch_model:
branch_model = str(branch_model)
tree.run_model(branch_model)
print(tree.get_evol_model(branch_model))
### site model
for site_model in site_models:
tree.run_model(site_model)
#tree.run_model('SLR.lele')
global evol_output_dir, final_evol_tree
evol_output_dir = workir
final_evol_tree = evol_output_dir + '/tree_evol_result.png'
tree.render(final_evol_tree,
layout=evol_clean_layout,
histfaces=site_models)
return tree
def tree_layout(tree_file, ps_node_list):
t = EvolTree(tree_file, format=0)
style_other = NodeStyle()
style_other['size'] = 6
style_ps = NodeStyle()
style_ps['fgcolor'] = '#ff0000'
style_ps['size'] = 6
for node in t.iter_descendants():
descendant = t.get_descendant_by_node_id(node.node_id)
if node.node_id in ps_node_list:
descendant.img_style = style_ps
else:
descendant.img_style = style_other
ts = TreeStyle()
ts.layout_fn = layout
ts.show_branch_support = False
ts.show_branch_length = False
ts.show_leaf_name = False
result_picture = os.path.join(output_dir, 'positive_selection_tree.png')
t.render(result_picture, tree_style=ts)
