tabulate_gene_tree

tabulate.py

def tabulate_names(tree):
	cladenames={}
	for idx, clade in enumerate(tree.find_clades()):
		if clade.name:
			clade.name = '%d_%s' % (idx, clade.name)
		else:
			clade.name = str(idx)
			cladenames[clade.name] = clade
return cladenames
        
genefamily = {}
names = lookup_by_names(tree)
for gene in tree.get_terminals():
	clade = names[gene]
	if clade in genefamily:
		genefamily[clade] +=1
	else:
		names[clade] =1