How to use the prophyle.newick2makefile.TreeIndex function in prophyle

args = parser.parse_args()

	k=args.k
	assert k>0
	newick_fn=args.newick_fn
	output_dir_fn=args.output_dir_fn
	library_dir_fn=args.library_dir_fn
	r=args.r

	#logger.info("Starting index construction")
	#logger.info("       newick : {}".format(newick_fn))
	#logger.info("   output dir : {}".format(output_dir_fn))
	#logger.info("            k : {}".format(k))

	ti=TreeIndex(
			tree_newick_fn=newick_fn,
			library_dir=library_dir_fn,
			index_dir=output_dir_fn,
		)
	ti.build_index(
			k=k,
			mask_repeats=r,
		)