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

def assign_all_reads(
    tree_fn,
    inp_fo,
    kmer_lca,
    tie_lca,
    form,
    k,
    measure,
    annotate,
):
    assert form in ["kraken", "sam"]
    assert k > 1

    tree_index = TreeIndex(
        tree_newick_fn=tree_fn,
        k=k,
    )

    if CONFIG['DIAGNOSTICS']:
        tree_index.diagnostics()

    assignment = Assignment(
        output_fo=sys.stdout,
        tree_index=tree_index,
        kmer_lca=kmer_lca,
        tie_lca=tie_lca,
        annotate=annotate,
    )

    if form == "sam":

def assign_all_reads(
    tree_fn,
    inp_fo,
    kmer_lca,
    tie_lca,
    form,
    k,
    measure,
    annotate,
):
    assert form in ["kraken", "sam"]
    assert k > 1

    tree_index = TreeIndex(
        tree_newick_fn=tree_fn,
        k=k,
    )

    if CONFIG['DIAGNOSTICS']:
        tree_index.diagnostics()

    assignment = Assignment(
        output_fo=sys.stdout,
        tree_index=tree_index,
        kmer_lca=kmer_lca,
        tie_lca=tie_lca,
        annotate=annotate,
    )

    if form == "sam":