def load_json(fp):
data = json.loads(clean_json(fp))
taxonomy = {}
count_total = 0
counts = []
for row in data['ubiome_bacteriacounts']:
normalise_row(row)
counts.append(row['count_norm'])
t = PhyloTree()
t.name = row['tax_name']
t.add_features(**row)
taxonomy[row['taxon']] = t
root = taxonomy[min(taxonomy.keys())]
count_total = root.count_norm
root.alpha = alpha_function(counts)
for t in taxonomy.values():
t.add_feature('count_pct', float(t.count_norm) / count_total * 100)
parent = t.parent
tp = taxonomy.get(parent)
if tp is not None:
tp.add_child(t)
print('loaded {} into tree depth {} diversity {:.2f}'.format(
len(taxonomy), len(root), root.alpha))
return root
def build_tree(self, sample, rank_limit='None'):
# Gets taxids of sample. Gets all taxids if sample is None.
taxids = set(self.get_all_tax_ids(sample))
taxid2nodes = {}
all_nodes = {}
root_children = []
for taxid in taxids:
taxid2nodes[taxid] = []
taxpath = self.get_taxpath(taxid)
rank = self.get_rank(taxid)
if self.rank_position[rank] <= self.rank_position[rank_limit]:
for node_id in taxpath:
if node_id != '':
if node_id not in all_nodes:
node = all_nodes.setdefault(node_id, PhyloTree())
node.name = str(node_id)
node.taxid = node_id
rank = self.get_rank(node_id)
node.add_feature("rank", rank)
node.add_feature("sci_name", self.get_name(node_id))
if rank == 'superkingdom':
root_children.append(node)
else:
node = all_nodes[node_id] # node already exists
taxid2nodes[taxid].append(node)
# generate parent child relationships
for taxid in taxid2nodes.keys():
parent = None
for node in taxid2nodes[taxid]:
if parent and node not in parent.children:
parent.add_child(node)
parent = node
root = PhyloTree()
root.name = 'root'
root.taxid = '0'
root.add_feature("rank", "root")
root.add_feature("sci_name", "root")
for child in root_children:
root.add_child(child)
tree = root
if len(root.children) == 1:
tree = root.children[0].detach()
return tree
