last_common_ancestor.py 文件源码

def build_lca_map(gen: typing.Iterator, tree: Taxonomy) -> dict:
    """
    Build a last common ancestor dictionary
    :param sam_inf: path to SAM infile
    :param extract_ncbi_tid: function to extract ncbi_tid
    :param tree: NCBITree
    :return: dict key (query name: string) value (ncbi_tid: int)
    """
    lca_map = {}
    for qname, rname in gen:
        tax = tree(rname)
        if qname in lca_map:
            current_tax = lca_map[qname]
            if current_tax:
                if current_tax != tax:
                    lca_map[qname] = least_common_ancestor((tax, current_tax))
        else:
            lca_map[qname] = tax
    return lca_map