def open_tree(tree_file_path):
"""Opens tree (contree or treefile) and assigns support values to nodes in case of a standard tree file"""
if 'contree' in tree_file_path:
tree = PhyloTree(tree_file_path, sp_naming_function=None)
elif 'treefile' in tree_file_path: # Branch supports in SH-aLRT support (%) / ultrafast bootstrap support (%)
tree = PhyloTree(tree_file_path, sp_naming_function=None, format=1)
for node in tree.iter_descendants():
if not node.is_leaf():
support_values = node.name.split('/')
try:
node.support = float(support_values[1])
except IndexError: # No support values when sequences were identical --> set support artifically to 100.0
node.support = 100.0
#node.add_features(shalrt = float(support_values[0])) # Not necessary...
else:
sys.exit('Error: tree format not recognised')
return tree
t = PhyloTree('temp/queryCOG.hmmhits.fasta.aln.trimal.treefile')
# try to root with largest paralog clade
try:
m = 0
for clade in t.get_monophyletic(values=["c", "b"],
target_attr="annot"):
if len([l for l in clade.get_leaves()]) > m:
rooting_clade = clade
m = len([l for l in clade.get_leaves()])
t.set_outgroup(clade)
except:
midpoint = t.get_midpoint_outgroup()
if midpoint: t.set_outgroup(midpoint)
annotate_leaf_proteins(t)
# find the clade with the mapped sequence
for l in t.iter_descendants():
if l.name == mapped_seq:
clade = l
n = 0
while n == 0:
if clade.up:
annotations = [
leaf.annot for sister in clade.get_sisters()
for leaf in sister.get_leaves()
]
counts = dict(Counter(annotations))
if 'c' not in counts.keys():
counts['c'] = 0
if ('a' in annotations) and (
counts['a'] / (counts['a'] + counts['c']) > 0.15):
clade = clade.up
