def insert(scores, threshold, length_f=None):
"""Insert nodes that pass the threshold
Parameters
----------
scores : dict
The result of best()
threshold : float
A minimum scoring threshold which must be exceeded for a node to be
inserted
length_f : function, optional
A function which can provide a branch length to set. This function
must conform to the following signature:
f(TreeNode, str, float) -> float
Where TreeNode is the node to insert at, str is the name of the node
being inserted, and float is the score of the query at the node.
The default is to set a branch length of 0.0
"""
if length_f is None:
def length_f(a, b, c):
return 0.0
for query, result in scores.items():
if result['score'] >= threshold:
length = length_f(result['node'], query, result['score'])
result['node'].append(skbio.TreeNode(name=query, length=length))
def recursive_subdivide(node, k, count, id_1, tree_node):
count += 1
id_1 += str(count)
bin_id.append("H" + str(count))
samples["H" + str(count)] = ""
if len(node.points)<=k:
return
print(type(node.width))
w_ = node.width/2
h_ = node.height/2
#fun challenge do it in a for loop
#probably make it smaller
p = contains(node.x0, node.y0, w_, h_, node.points)
x1 = Node(node.x0, node.y0, w_, h_, p, id_1 + "sw;")
node_1 = skbio.TreeNode(name=str(count) + "sw")
for pt in p:
bin_1.append((pt.sample_id, count, x1.get_id()))
node_1.extend([skbio.TreeNode(name=pt.sample_id)])
recursive_subdivide(x1, k, count, id_1+"sw;", node_1)
p = contains(node.x0, node.y0+h_, w_, h_, node.points)
x2 = Node(node.x0, node.y0+h_, w_, h_, p, id_1+"nw;")
node_2 = skbio.TreeNode(name=str(count)+"nw")
for pt in p:
bin_1.append((pt.sample_id, count, x2.get_id()))
node_2.extend([skbio.TreeNode(name=pt.sample_id)])
recursive_subdivide(x2, k, count, id_1+"nw;", node_2)
p = contains(node.x0+w_, node.y0, w_, h_, node.points)
x3 = Node(node.x0 + w_, node.y0, w_, h_, p, id_1+"se;")
node_3 = skbio.TreeNode(name=str(count)+"se")
for pt in p:
bin_1.append((pt.sample_id, count, x3.get_id()))
node_3.extend([skbio.TreeNode(name=pt.sample_id)])
recursive_subdivide(x3, k, count, id_1+"se;", node_3)
p = contains(node.x0+w_, node.y0+h_, w_, h_, node.points)
x4 = Node(node.x0+w_, node.y0+h_, w_, h_, p, id_1+"ne;")
node_4 = skbio.TreeNode(name=str(count)+"ne")
for pt in p:
bin_1.append((pt.sample_id, count, x4.get_id()))
node_4.extend([skbio.TreeNode(name=pt.sample_id)])
recursive_subdivide(x4, k, count, id_1+"ne;", node_4)
tree_node.extend([node_1, node_2, node_3, node_4])
node.children = [x1, x2, x3, x4]
def _0(ff: TSVTaxonomyFormat) -> skbio.TreeNode:
root = skbio.TreeNode('root', length=0)
with ff.open() as fh:
reader = iter(csv.reader(fh, delimiter='\t'))
next(reader) # skip header
for row in reader:
id_, taxonomy = row[:2]
taxonomy = taxonomy.split(';')
node = root
for taxon in taxonomy:
for child in node.children:
if child.name == taxon:
node = child
break
else:
child = skbio.TreeNode(taxon, length=1)
node.append(child)
node = child
node.append(skbio.TreeNode(id_, length=1))
return root
def subdivide(self, count):
samples = pd.DataFrame()
samples['index'] = df['index']
samples = samples.set_index('index')
count = 0
id_1 = ""
base = skbio.TreeNode(name="root")
recursive_subdivide(self.root, self.threshold, count, id_1, base)
return base
def tree_to_matrix(tree, label, with_repr=False):
# to do here : given a skbio tree and the beta-labels in a given order,
# return the matrix A and the new labels corresponding
dicti = dict()
d = len(label)
LEAVES = [tip.name for tip in tree.tips()]
order = []
# list that will give the order in which the nodes are added
# in the dicti, such that it will be easy to remove similar nodes
for i, name_leaf in enumerate(label):
name_leaf = label[i]
dicti[name_leaf] = np.zeros(d, dtype=bool)
dicti[name_leaf][i] = True
order.append(name_leaf)
if name_leaf not in LEAVES:
tree.append(skbio.TreeNode(name=name_leaf)
) # add the node if it is node already in the tree
print("The feature {} i not in the leaves of the tree".format(
name_leaf))
for n in tree.find(name_leaf).ancestors():
ancest = n.name
if ancest[-1] != "_":
if ancest not in dicti:
dicti[ancest] = np.zeros(d, dtype=bool)
order.append(ancest)
dicti[ancest][i] = True
L, label2 = [], []
for node in tree.levelorder():
nam = node.name
if nam in dicti and nam not in label2:
label2.append(nam)
L.append(dicti[nam])
to_keep = np.ones(len(L), dtype=bool)
to_keep = remove_same_vect(L, label2, order)
L = np.array(L)
to_keep[np.all(L, axis=1)] = False
return L[to_keep].T, np.array(label2)[to_keep]
def generate_new_phylogeny(phylogeny_fp, pivot_mapping_dct):
tree = average_branch_lengths(phylogeny_fp)
observed_internal_nodes = set()
for idx in pivot_mapping_dct.keys():
if idx == -1:
continue
else:
node_lca = tree.lca(pivot_mapping_dct[idx])
if len(list(node_lca.tips())) != len(pivot_mapping_dct[idx]):
raise ValueError("The LCA has different tips than expected",
len(list(node_lca.tips())),
len(pivot_mapping_dct[idx]))
tmp_node = skbio.TreeNode('cluster' + str(idx))
tmp_node.length = node_lca.avg
parent_node = node_lca.parent
if node_lca.dummy_name in observed_internal_nodes:
raise ValueError("node_lca was observed before!",
node_lca.dummy_name, node_lca, idx)
else:
observed_internal_nodes.add(node_lca.dummy_name)
parent_node.append(tmp_node)
parent_node.remove(node_lca)
return tree
def majority_consensus(trees, cutoff=0.5):
"""Compute the majority consensus tree.
When a taxon is designated as an outgroup, this algorithm is equivalent to
tree popping described in The Mathematics of Phylogenetics. Since a clade
is the subset of a split that does not contain the root, all sets of
terminal labels obtained via the tips method when traversing the tree
correspond to the half of the split without the root. Thus operating on the
clades is implicitly operating on the equivalent split.
The overall approach of the algorithm is to first tally the clades and
then to progressively build the consensus tree by applying the clades in
decreasing order of frequency (as long as they are compatible with all
clades already displayed on the tree). The proof presented in The
Mathematics of Phylogenetics is considerably more complex than the more
intuitive algorithm used here. Whereas that proof required finding the
minimum spanning tree, this approach instead uses the idea that as long as
clades are applied in order of size (which is guaranteed by the principle
that a parent clade will appear at least as many times in counts as its
subclades and subsequent sorting on counts then size), then the right node
onto which to apply a clade is always the smallest one that is compatible.
This actually equivalent to finding the minimum spanning tree of the nodes
colored by each clade (blue for those in the clade and red for those not in
the clade). The tree induced by a node whose terminals are a superset of
the clade clearly spans that clade. Thus, by iterating through all the
nodes in the consensus tree sorted by decreasing size, the last node that
meets this criterion induces the minimal spanning tree (MST) for the blue
nodes (those within the clade). The MST for the red nodes (those not within
the clade and containing the root) intersects with this MST at a single
node via the tree popping theorem. By maintaining the directionality of the
parent-child relationships away from the root, we know this is the node we
have already identified. To see why, assume another node in the blue MST is
the node of intersection. The parent of this node must also be blue because
otherwise the MST is not minimal.The parent must also lie on the red MST
since by construction following the chain of parents creates a path to the
root and this path to the root must be on the red MST as trees have no
cycles. Thus, we have a contradiction of the blue and red MSTs only
intersecting at a single node, so the intersection node must be the
previously identified node.
Parameters
----------
trees: list of skbio TreeNodes
Input trees from which to compute the consensus.
cutoff: float
The minimum fraction of trees a clade must be displayed on in order
(not including the value itself) to contribute to the consensus.
The default value of 0.5 ensures all incorporated clades are
compatible. If the cutoff is set lower, a clade is only added to
the consensus if it compatible with all clades already displayed.
Clades are added in order of decreasing number of counts in the
input trees.
Returns
-------
root: TreeNode
"""
# Count nodes and record tip names
counts, tip_names = {}, set()
for tree in trees:
tip_names.update([tip.name for tip in tree.tips()])
for node in tree.traverse():
if not node.is_tip():
tip_set = frozenset([tip.name for tip in node.tips()])
counts[tip_set] = counts.get(tip_set, 0) + 1
counts = sorted(counts.items(),
key=lambda x: (x[1], len(x[0])),
reverse=True) # Sort by count then size
# Make count list and node dictionary
# Initialize consensus nodes with a tip for each unique taxon label and a root node containing all these tips
# (The tips are instantiated first, and then the root node containing them is created.)
consensus_nodes = {
frozenset([name]): skbio.TreeNode(name=name)
for name in tip_names
}
root = skbio.TreeNode(children=list(consensus_nodes.values()))
consensus_nodes[frozenset([node.name for node in root.children])] = root
# Add nodes
for tip_set1, count in counts[1:]:
if count / len(trees) < cutoff:
break
# Find parent
for tip_set2 in sorted(consensus_nodes,
key=lambda x: len(x),
reverse=True):
compatible = (tip_set1 <= tip_set2 or tip_set2 <= tip_set1
or not (tip_set1 & tip_set2))
if not compatible:
break # Break search over parents
if tip_set2 >= tip_set1:
parent_set = tip_set2 # Smallest superset since sorted by size
if not compatible:
continue # Each clade should be compatible with all others in consensus tree
parent_node = consensus_nodes[parent_set]
# Construct current node
children = []
for node in parent_node.children:
for tip in node.tips(include_self=True):
if tip.name in tip_set1:
children.append(node)
break # Compatibility requires all tips of a subnode are included if one is
node = skbio.TreeNode(
children=children, support=count /
len(trees)) # Instantiation automatically updates parents
consensus_nodes[tip_set1] = node
parent_node.append(node)
# Get branch lengths
bl_sums = {}
for tree in trees:
for node in tree.traverse():
if node.is_tip():
continue
tip_set = frozenset([tip.name for tip in node.tips()])
# Add clade
if tip_set in consensus_nodes:
count, bl_sum = bl_sums.get(tip_set, (0, 0))
count, bl_sum = count + 1, bl_sum + node.length if node.length else None
bl_sums[tip_set] = (count, bl_sum)
# Add terminal children of clade
# The lengths of terminal children are only included if all the non-terminal children are clades
# displayed in the consensus tree. This is expressed by checking this condition in a for loop and
# proceeding to the else clause only if the loop isn't broken
for child_node in filter(lambda x: not x.is_tip(),
node.children):
if not frozenset([tip.name for tip in child_node.tips()
]) in consensus_nodes:
break
else:
for child_tip in filter(lambda x: x.is_tip(),
node.children):
tip_set = frozenset([child_tip.name])
count, bl_sum = bl_sums.get(tip_set, (0, 0))
count, bl_sum = count + 1, bl_sum + child_tip.length if child_tip.length else None
bl_sums[tip_set] = (count, bl_sum)
# Set branch lengths
for tip_set, (count, bl_sum) in bl_sums.items():
node = consensus_nodes[tip_set]
node.length = bl_sum / count if bl_sum else None
return root
def build_tree_recurse(gene_tree, path):
loss_nodes = []
current_tree = gene_tree
path_splited = path.split('_')
_id = '_' + path.split('_')[-1] if len(path_splited) > 1 else ''
parent_name_splited = gene_tree.name.split('_')
_parent_id = '_' + parent_name_splited[-1] if len(
parent_name_splited) > 1 else ''
for i in range(len(parent_name_splited)):
if ('l' in parent_name_splited[i]
and len(parent_name_splited[i]) == 2):
_parent_id = '_' + parent_name_splited[i - 1] if i > 1 else ''
break
if (_id):
subtree_path = os.path.join(path, 'gene_tree.txt')
f = open(subtree_path)
subtree = skbio.read(f, format='newick', into=skbio.tree.TreeNode)
f.close()
current_tree = subtree
event_path = os.path.join(path, 'event.txt')
f = open(event_path)
line = f.readline()
splited = line.strip().split(',')
node_name = splited[0]
distance = float(splited[1])
event_name = '_' + splited[2][0]
event_index = '_' + splited[3]
new_dt_node = skbio.TreeNode()
child = None
for node in gene_tree.traverse():
if node.name == (node_name + _parent_id):
child = node
break
elif (node.name):
if '_dl' in node.name:
if node.name.split('_dl')[0] == (node_name + _parent_id):
child = node
break
elif '_tl' in node.name:
if node.name.split('_tl')[0] == (node_name + _parent_id):
child = node
break
elif '_il' in node.name:
if node.name.split('_il')[0] == (node_name + _parent_id):
child = node
break
elif '_sl' in node.name:
if node.name.split('_sl')[0] == (node_name + _parent_id):
child = node
break
parent = child.parent
new_dt_node.name = node_name + event_name + _id
new_dt_node.length = child.length - distance
new_dt_node.parent = parent
new_dt_node.children.append(child)
child.length = distance
child.parent = new_dt_node
for i in range(len(parent.children)):
if (parent.children[i].name == child.name):
del parent.children[i]
break
parent.children.append(new_dt_node)
new_dt_node.children.append(subtree)
subtree.parent = new_dt_node
for node in subtree.traverse():
node.name = node.name + _id
files = os.listdir(path)
files_end_with_digit = []
for f in files:
if f.split('_')[-1].isdigit():
files_end_with_digit.append(f)
files = files_end_with_digit
files = sorted(files, key=lambda x: int(x.split('_')[-1]))
for f in files:
file_path = os.path.join(path, f)
if os.path.isdir(file_path):
loss_nodes += build_tree_recurse(current_tree, file_path)
files = os.listdir(path)
for f in files:
file_name = f.split('_')
if (file_name and file_name[0] == 'ils'):
_index = '_' + file_name[1]
ils_path = os.path.join(path, f)
file_ = open(ils_path)
line = file_.readline()
splited = line.split(',')
node_name = splited[0]
for node in current_tree.traverse():
if node.name == (node_name + _id):
node.name = node_name + '_i' + _index + '_id' + _id
break
file_.close()
for f in files:
file_name = f.split('_')
if (file_name and file_name[0] == 's'):
_index = '_' + file_name[1]
s_path = os.path.join(path, f)
file_ = open(s_path)
line = file_.readline()
splited = line.split(',')
node_name = splited[0]
for node in current_tree.traverse():
if node.name == (node_name + _id):
node.name = node_name + '_s' + _index + '_id' + _id
break
file_.close()
for f in files:
file_name = f.split('_')
if (file_name and file_name[0] == 'loss'):
loss_path = os.path.join(path, f)
file_ = open(loss_path)
line = file_.readline()
splited = line.split(',')
node_l_name = splited[0]
node_l_distance = float(splited[1])
node_index = int(splited[2])
new_l_node = skbio.TreeNode()
child = None
print('start')
for node in current_tree.traverse():
if (node.name):
print('n=', node.name)
splited = node.name.split('_')
if (_id == ''):
if (splited[0] == node_l_name):
child = node
break
else:
if node.name == (node_l_name + _id):
child = node
break
elif (splited[0] == node_l_name
and ('_' + splited[-1]) == _id):
child = node
break
elif '_dl' in node.name:
if node.name.split('_dl')[0] == (node_l_name + _id):
child = node
break
else:
splited = node.name.split('_dl')[0].split('_')
elif '_tl' in node.name:
if node.name.split('_tl')[0] == (node_l_name + _id):
child = node
break
else:
splited = node.name.split('_tl')[0].split('_')
elif '_il' in node.name:
if node.name.split('_il')[0] == (node_l_name + _id):
child = node
break
else:
splited = node.name.split('_il')[0].split('_')
elif '_sl' in node.name:
if node.name.split('_sl')[0] == (node_l_name + _id):
child = node
break
else:
splited = node.name.split('_sl')[0].split('_')
if (splited[0] == node_l_name
and ('_' + splited[-1]) == _id):
child = node
break
print(node_l_name + _id)
print('end')
parent = child.parent
if '_s_' in parent.name:
new_l_node.name = node_l_name + '_l' + '_id' + _id
if (parent.children[0].name == child.name):
parent.children[
1].name += '_sl' + '_ind_' + parent.name.split(
'_s_')[1].split('_')[0] + '_' + str(node_index)
else:
parent.children[
0].name += '_sl' + '_ind_' + parent.name.split(
'_s_')[1].split('_')[0] + '_' + str(node_index)
elif '_d_' in parent.name:
new_l_node.name = node_l_name + '_l' + '_id' + _id
if (parent.children[0].name == child.name):
parent.children[
1].name += '_dl' + '_ind_' + parent.name.split(
'_d_')[1].split('_')[0] + '_' + str(node_index)
else:
parent.children[
0].name += '_dl' + '_ind_' + parent.name.split(
'_d_')[1].split('_')[0] + '_' + str(node_index)
elif '_t_' in parent.name:
new_l_node.name = node_l_name + '_l' + '_id' + _id
if (parent.children[0].name == child.name):
parent.children[
1].name += '_tl' + '_ind_' + parent.name.split(
'_t_')[1].split('_')[0] + '_' + str(node_index)
else:
parent.children[
0].name += '_tl' + '_ind_' + parent.name.split(
'_t_')[1].split('_')[0] + '_' + str(node_index)
elif '_i_' in parent.name:
new_l_node.name = node_l_name + '_l' + '_id' + _id
if (parent.children[0].name == child.name):
parent.children[
1].name += '_il' + '_ind_' + parent.name.split(
'_i_')[1].split('_')[0] + '_' + str(node_index)
else:
parent.children[
0].name += '_il' + '_ind_' + parent.name.split(
'_i_')[1].split('_')[0] + '_' + str(node_index)
new_l_node.length = child.length - node_l_distance
new_l_node.parent = parent
new_l_node.children.append(child)
child.length = node_l_distance
child.parent = new_l_node
for i in range(len(parent.children)):
if (parent.children[i].name == child.name):
del parent.children[i]
break
parent.children.append(new_l_node)
loss_nodes.append(new_l_node)
file_.close()
return loss_nodes
