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

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":
        assignment.print_sam_header()

    for krakline in inp_fo:
        assignment.process_read(krakline, form=form, measure=measure)

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":
        assignment.print_sam_header()

    for krakline in inp_fo:
        assignment.process_read(krakline, form=form, measure=measure)