def _convert_consensus_paths_to_affinity_tree_nodes():
at_nodes = []
assigned_sequences = []
for c_id, c_info in consensus_paths.items():
assigned_sequences += c_info.assigned_sequences_ids
all_seq = p.get_sequences_ids()
compatibilities = p.get_compatibilities(all_seq, c_info.path)
if len(c_info.assigned_sequences_ids):
assigned_seq_comp = [c
for seq_id, c in compatibilities.items()
if seq_id in c_info.assigned_sequences_ids]
mincomp = min(assigned_seq_comp)
else:
mincomp = 0
new_node = tree.AffinityNode(id_=tree.AffinityNodeID(c_id + 1),
parent=tree.AffinityNodeID(0),
sequences=c_info.assigned_sequences_ids,
mincomp=mincomp,
compatibilities=compatibilities,
consensus=c_info.path,
children=[])
at_nodes.append(new_node)
node_for_unassigned_sequences = tree.AffinityNode(parent=tree.AffinityNodeID(0),
sequences=[seq_id
for seq_id in p.get_sequences_ids()
if seq_id not in assigned_sequences],
id_=tree.AffinityNodeID(len(at_nodes) + 1),
mincomp=graph.Compatibility(0),
children=[])
at_nodes.append(node_for_unassigned_sequences)
return at_nodes
def _get_children_nodes_looping(node: tree.AffinityNode,
poagraph: graph.Poagraph,
output_dir: Path,
blosum_path: Path,
p: parameters.P,
current_max_affinity_node_id: int) -> List[tree.AffinityNode]:
"""Generates children of given Affinity Tree node."""
children_nodes: List[tree.AffinityNode] = []
not_assigned_sequences_ids: List[msa.SequenceID] = node.sequences
detailed_logger.info(f"""Getting children nodes for
affinity node {node.id_}...""")
affinity_node_id = 0
so_far_cutoffs: List[poagraph.Compatibility] = []
while not_assigned_sequences_ids:
detailed_logger.info(f"### Getting child {len(so_far_cutoffs)}...")
child_ready = False
attempt = 0
current_candidates = not_assigned_sequences_ids
while not child_ready:
consensus_candidate = poa.get_consensuses(poagraph,
current_candidates,
output_dir,
f"parent_{node.id_}_child_{len(so_far_cutoffs)}_attempt_{attempt}",
blosum_path,
parameters.Hbmin(0),
specific_consensuses_id=[0])[0].path
compatibilities_to_consensus_candidate = poagraph.get_compatibilities(sequences_ids=not_assigned_sequences_ids,
consensus_path=consensus_candidate,
p=p)
compatibilities_to_consensus_candidate[msa.SequenceID("parent")] = node.mincomp
qualified_sequences_ids_candidates, cutoff = _get_qualified_sequences_ids_and_cutoff(
compatibilities_to_max_c=compatibilities_to_consensus_candidate,
so_far_cutoffs=so_far_cutoffs,
splitted_node_id=node.id_)
if qualified_sequences_ids_candidates == current_candidates or attempt == 10:
if attempt == 10:
detailed_logger.info("Attempt treshold 10 exceeded!")
affinity_node_id += 1
affinity_node = tree.AffinityNode(
id_=tree.AffinityNodeID(current_max_affinity_node_id + affinity_node_id),
parent=node.id_,
sequences=qualified_sequences_ids_candidates,
mincomp=_get_min_comp(node_sequences_ids=qualified_sequences_ids_candidates,
comps_to_consensus=compatibilities_to_consensus_candidate),
consensus=graph.SeqPath(consensus_candidate))
children_nodes.append(affinity_node)
not_assigned_sequences_ids = list(set(not_assigned_sequences_ids) - set(qualified_sequences_ids_candidates))
child_ready = True
so_far_cutoffs.append(affinity_node.mincomp)
else:
current_candidates = qualified_sequences_ids_candidates
attempt += 1
detailed_logger.info("Children nodes generated.")
return children_nodes
def _get_root_node(poagraph: graph.Poagraph,
blosum_path: Path,
output_dir: Path,
p: parameters.P) -> tree.AffinityNode:
"""Creates root node of the Affinity Tree.
The node has assigned a consensus path and
all sequences present in poagraph."""
detailed_logger.info("Getting the root affinity node...")
all_poagraph_sequences_ids = poagraph.get_sequences_ids()
try:
consensus_paths = poa.get_consensuses(poagraph,
all_poagraph_sequences_ids,
output_dir,
"root",
blosum_path,
hbmin=parameters.Hbmin(0),
specific_consensuses_id=[0])
except poa.NoConsensusError:
raise AffinityTreeBuildException("Cannot find root consensus.")
compatibilities = poagraph.get_compatibilities(all_poagraph_sequences_ids,
consensus_paths[0].path,
p=p)
affinity_node = tree.AffinityNode(id_=tree.AffinityNodeID(0),
sequences=[*poagraph.sequences.keys()],
mincomp=_get_min_comp(all_poagraph_sequences_ids, compatibilities),
compatibilities=compatibilities,
consensus=consensus_paths[0].path)
detailed_logger.info(f"New affinity node created: {str(affinity_node)}")
return affinity_node
def build_poa_affinity_tree(p: graph.Poagraph,
blosum: Optional[parameters.Blosum],
output_dir: Path,
hbmin: parameters.Hbmin,
verbose: bool) -> tree.AffinityTree:
"""Builds Affinity Tree coherent with poa software.
This method builds a simple version of Affinity Tree
as it uses a single call to poa software. Poa provides
division of sequences in Poagraph into consistent groups
with a consensus path assigned to each group. These groups
are converted in this method to Affinity Tree nodes and
connected with a dummy root node so the result is coherent
with pangtree definition of Affinity Tree.
Args:
p: Poagraph containing sequences to be divided into
groups (Affinity Tree nodes).
optional blosum: BLOSUM matrix. If not provided, default Blosum80.mat is used.
output_dir: Path to a directory that can be used by poa software.
hbmin: Parameter required by poa software. The minimum value of
sequence compatibility to generated consensus.
verbose: Switch to control logging intensity.
Raises:
AffinityTreeGenerationException: if consensuses cannot be found.
"""
def _convert_consensus_paths_to_affinity_tree_nodes():
at_nodes = []
assigned_sequences = []
for c_id, c_info in consensus_paths.items():
assigned_sequences += c_info.assigned_sequences_ids
all_seq = p.get_sequences_ids()
compatibilities = p.get_compatibilities(all_seq, c_info.path)
if len(c_info.assigned_sequences_ids):
assigned_seq_comp = [c
for seq_id, c in compatibilities.items()
if seq_id in c_info.assigned_sequences_ids]
mincomp = min(assigned_seq_comp)
else:
mincomp = 0
new_node = tree.AffinityNode(id_=tree.AffinityNodeID(c_id + 1),
parent=tree.AffinityNodeID(0),
sequences=c_info.assigned_sequences_ids,
mincomp=mincomp,
compatibilities=compatibilities,
consensus=c_info.path,
children=[])
at_nodes.append(new_node)
node_for_unassigned_sequences = tree.AffinityNode(parent=tree.AffinityNodeID(0),
sequences=[seq_id
for seq_id in p.get_sequences_ids()
if seq_id not in assigned_sequences],
id_=tree.AffinityNodeID(len(at_nodes) + 1),
mincomp=graph.Compatibility(0),
children=[])
at_nodes.append(node_for_unassigned_sequences)
return at_nodes
global_logger.info("POA defined affinity tree generation started.")
if blosum is None:
blosum = get_default_blosum()
_raise_error_if_invalid_poagraph(p)
try:
consensus_paths = poa.get_consensuses(p,
p.get_sequences_ids(),
output_dir,
"poa_tree",
blosum.filepath,
hbmin)
except poa.NoConsensusError:
raise AffinityTreeBuildException("No consensus in the Affinity Tree.")
consensus_nodes = _convert_consensus_paths_to_affinity_tree_nodes()
root_node = tree.AffinityNode(id_=tree.AffinityNodeID(0),
children=[c_node.id_
for c_node in consensus_nodes])
affinity_tree = tree.AffinityTree([root_node] + consensus_nodes)
global_logger.info("POA defined affinity tree generation finished.")
return affinity_tree
