kmeans = KMeans(n_clusters=2,
random_state=0,
precompute_distances=True,
tol=1e-10).fit(dis.values)
kmeans.labels_
id2info = defaultdict(list)
for idx, id in enumerate(dis.index):
new_name = convert_genome_ID_rev(id.split('_')[0]) + '_' + id
id2info[new_name] = [str(kmeans.labels_[idx])]
from api_tools.itol_func import *
text = to_binary_shape(id2info, {'1': {}, '0': {}})
with open('../itol_txt/separate_tmp.txt', 'w') as f1:
f1.write(text)
t = PhyloTree(intree)
# t.set_outgroup(t.get_midpoint_outgroup())
t.set_species_naming_function(
lambda node: convert_genome_ID_rev(node.name.split('_')[0]))
print(t.get_ascii(attributes=["name", "species"], show_internal=False))
t2 = t.collapse_lineage_specific_expansions()
ntrees, ndups, sptrees = t2.get_speciation_trees()
sptrees = list(sptrees)
print("Found %d species trees and %d duplication nodes" % (ntrees, ndups))
for spt in sptrees:
print(len(spt.get_leaf_names()))
