Python Tree.nodes方法代码示例

# 需要导入模块: from dendropy import Tree [as 别名]
# 或者: from dendropy.Tree import nodes [as 别名]
def match_ancestors_across_models(con):
    """This method fills data in the table AncestorsAcrossModels"""
    cur = con.cursor()

    modelids = get_phylo_modelids(con)
    msaids = get_alignment_method_ids(con)

    ancid_childrenids = {}  # key = Ancestor ID, value = list of Taxa IDs

    """Pull the map of taxon names to IDs from the database.
        We'll access this information a lot, so let's save it in a separate hashtable
        rather than repeatedly querying the databse."""
    taxonname_id = {}
    sql = "select id, shortname from Taxa"
    cur.execute(sql)
    for ii in cur.fetchall():
        id = ii[0]
        name = ii[1]
        taxonname_id[name] = id

    for modelid in modelids:
        for msaid in msaids:
            sql = "select newick from AncestralCladogram where unsupportedmltreeid in (select id from UnsupportedMlPhylogenies where almethod=" + msaid.__str__(
            ) + " and phylomodelid=" + modelid.__str__() + ")"
            cur.execute(sql)
            xx = cur.fetchone()
            if xx is None:
                write_error(con, "I cannot find the ancestral Newick cladogram for almethod=" +
                            msaid.__str__() + " and phylomodelid=" + modelid.__str__())
            cladonewick = xx[0].__str__()

            t = Tree()
            t.read_from_string(cladonewick, "newick")

            for node in t.nodes():
                if node.is_leaf() == False and node.level() > 0:
                    sql = "select id from Ancestors where name='Node" + node.label + \
                        "' and almethod=" + msaid.__str__() + " and phylomodel=" + modelid.__str__()
                    cur.execute(sql)
                    ancid = cur.fetchone()[0]
                    ancid_childrenids[ancid] = []

                    for l in node.leaf_iter():
                        # print "978:", l
                        taxonname = l.as_newick_string()
                        # print "980:", taxonname
                        taxonname = re.sub("'", "", taxonname)
                        ancid_childrenids[ancid].append(
                            taxonname_id[taxonname])

    # key = Ancestor ID, value = list of other ancestor IDs with the same
    # children.
    ancid_matches = {}
    for anc1 in ancid_childrenids:
        ancid_matches[anc1] = []
        mychildren = ancid_childrenids[anc1]
        mychildren.sort()
        for anc2 in ancid_childrenids:
            if anc1 == anc2:
                """Skip the self comparison."""
                continue
            theirchildren = ancid_childrenids[anc2]
            theirchildren.sort()
            if mychildren == theirchildren:
                ancid_matches[anc1].append(anc2)

    sql = "delete from AncestorsAcrossModels"
    cur.execute(sql)
    con.commit()

    for anc1 in ancid_matches:
        for anc2 in ancid_matches[anc1]:
            sql = "insert into AncestorsAcrossModels (ancid, same_ancid) values(" + anc1.__str__(
            ) + "," + anc2.__str__() + ")"
            cur.execute(sql)
    con.commit()