def build_bid_taxonomy_map(self):
self.bid_taxonomy_map = {}
self.ranks_set = set([])
for node in self.tax_tree.traverse("postorder"):
if not node.is_root() and hasattr(node, "B"):
parent = node.up
branch_rdiff = Taxonomy.lowest_assigned_rank_level(node.ranks) - Taxonomy.lowest_assigned_rank_level(
parent.ranks
)
branch_rank_id = Taxonomy.get_rank_uid(node.ranks)
branch_len = node.dist
self.bid_taxonomy_map[node.B] = (branch_rank_id, branch_rdiff, branch_len)
self.ranks_set.add(branch_rank_id)
def build_bid_taxonomy_map(self):
self.bid_taxonomy_map = {}
self.ranks_set = set([])
for node in self.tax_tree.traverse("postorder"):
if not node.is_root() and hasattr(node, "B"):
parent = node.up
branch_rdiff = Taxonomy.lowest_assigned_rank_level(
node.ranks) - Taxonomy.lowest_assigned_rank_level(
parent.ranks)
branch_rank_id = Taxonomy.get_rank_uid(node.ranks)
branch_len = node.dist
self.bid_taxonomy_map[node.B] = (branch_rank_id, branch_rdiff,
branch_len)
self.ranks_set.add(branch_rank_id)
def label_bf_tree_with_ranks(self):
"""labeling inner tree nodes with taxonomic ranks"""
if not self.bf_rooted_tree:
raise AssertionError(
"self.bf_rooted_tree is not set: TaxTreeHelper.set_bf_unrooted_tree() must be called before!"
)
for node in self.bf_rooted_tree.traverse("postorder"):
if node.is_leaf():
seq_ranks = self.origin_taxonomy[node.name]
rank_level = Taxonomy.lowest_assigned_rank_level(seq_ranks)
node.add_feature("rank_level", rank_level)
node.add_feature("ranks", seq_ranks)
node.name += "__" + seq_ranks[rank_level]
else:
if len(node.children) != 2:
raise AssertionError(
"FATAL ERROR: tree is not bifurcating!")
lchild = node.children[0]
rchild = node.children[1]
rank_level = min(lchild.rank_level, rchild.rank_level)
while rank_level >= 0 and lchild.ranks[
rank_level] != rchild.ranks[rank_level]:
rank_level -= 1
node.add_feature("rank_level", rank_level)
node_ranks = [Taxonomy.EMPTY_RANK] * max(
len(lchild.ranks), len(rchild.ranks))
if rank_level >= 0:
node_ranks[0:rank_level + 1] = lchild.ranks[0:rank_level +
1]
node.name = lchild.ranks[rank_level]
else:
node.name = "Undefined"
if hasattr(node, "B"):
self.cfg.log.debug(
"INFO: empty taxonomic annotation for branch %s (child nodes have no common ranks)",
node.B)
node.add_feature("ranks", node_ranks)
self.tax_tree = self.bf_rooted_tree
self.init_taxnode_map()
def label_bf_tree_with_ranks(self):
"""labeling inner tree nodes with taxonomic ranks"""
if not self.bf_rooted_tree:
raise AssertionError(
"self.bf_rooted_tree is not set: TaxTreeHelper.set_bf_unrooted_tree() must be called before!"
)
for node in self.bf_rooted_tree.traverse("postorder"):
if node.is_leaf():
seq_ranks = self.origin_taxonomy[node.name]
rank_level = Taxonomy.lowest_assigned_rank_level(seq_ranks)
node.add_feature("rank_level", rank_level)
node.add_feature("ranks", seq_ranks)
node.name += "__" + seq_ranks[rank_level]
else:
if len(node.children) != 2:
raise AssertionError("FATAL ERROR: tree is not bifurcating!")
lchild = node.children[0]
rchild = node.children[1]
rank_level = min(lchild.rank_level, rchild.rank_level)
while rank_level >= 0 and lchild.ranks[rank_level] != rchild.ranks[rank_level]:
rank_level -= 1
node.add_feature("rank_level", rank_level)
node_ranks = [Taxonomy.EMPTY_RANK] * max(len(lchild.ranks), len(rchild.ranks))
if rank_level >= 0:
node_ranks[0 : rank_level + 1] = lchild.ranks[0 : rank_level + 1]
node.name = lchild.ranks[rank_level]
else:
node.name = "Undefined"
if hasattr(node, "B"):
self.cfg.log.debug(
"INFO: empty taxonomic annotation for branch %s (child nodes have no common ranks)", node.B
)
node.add_feature("ranks", node_ranks)
self.tax_tree = self.bf_rooted_tree
self.init_taxnode_map()
