Dendropy:在两个节点中间添加内部节点

Question

我对DendroPy非常陌生。我想要做的事情似乎很简单，但我不知道如何正确地做，我没有在互联网上找到任何东西。

我想在现有的树状树状树结构中，在两个节点之间添加一个节点。

from dendropy import Tree, Taxon, Node

t1 = Tree.get_from_string(
    "(((sp1: 0.35, sp2: 0.15):0.75, sp3:1): 0.5, (sp4: 0.5, sp5: 0.05)MRCA_sp4&sp5: 1)root;",
    "newick", rooting='force-rooted'
)
t1.print_plot()
mrca = t1.mrca(taxon_labels=["sp4", "sp5"])
print(mrca.description())

树和MRCA节点描述

正确地找到了sp4和sp5的MRCA。现在，我尝试在MRCA和root之间添加一个节点，使用下面的代码：

def add_node_midway_between_2_nodes(lowernode, taxon_label=None, node_label=None):
    newtaxon = Taxon(label=taxon_label)
    newnode = Node(taxon=newtaxon, label=node_label)
    newnode.parent_node = lowernode.parent_node
    newnode.edge_length = lowernode.edge_length/2
    lowernode.parent_node = newnode
    lowernode.edge_length = newnode.edge_length
    return newnode

node = add_node_midway_between_2_nodes(mrca, node_label="midway between root and MRCA sp4&sp5")
t1.print_plot()
str_t1 = t1.as_string(schema='newick')
print(str_t1)

根与MRCASP4&SP5之间有节点的树

&R根；

看了看情节和字符串，它似乎奏效了。但是，当我再次尝试计算sp4 et sp5的MRCA时，它不再找到“MRCASP4&SP5”，而是找到根节点。

mrca = t1.mrca(taxon_labels=["sp4", "sp5"])
print(mrca.description())

Output =根节点的描述

从parent_node到sp5，我仍然可以找到“MRCASP4&SP5”。

出于绝望，我尝试使用字符串str_t1重做树，但也没有工作，甚至给出了另一个结果(同样不正确)：节点“根和MRCA sp4&sp5之间的中间”。

t1 = Tree.get_from_string(
    str_t1,
    "newick", rooting='force-rooted'
)
mrca = t1.mrca(taxon_labels=["sp4", "sp5"])
print(mrca.description())

Output =节点“根到MRCASP4和SP5之间的中途”的描述

那么，在两个节点中间添加一个节点的干净方法是什么，这不会在之后创建奇怪的事件？

非常感谢

Answer 1

您的代码主要是工作的，但是您应该按照update_bipartitions中的建议，正确地应用树拓扑的任何更改。所以，在你的例子中，它看起来是这样的：

def add_node_midway_between_2_nodes(lowernode, taxon_label=None, node_label=None):
    newtaxon = Taxon(label=taxon_label)
    newnode = Node(taxon=newtaxon, label=node_label)
    newnode.parent_node = lowernode.parent_node
    newnode.edge_length = lowernode.edge_length/2
    lowernode.parent_node = newnode
    lowernode.edge_length = newnode.edge_length
    return newnode

node = add_node_midway_between_2_nodes(
    mrca, node_label="midway between root and MRCA sp4&sp5"
)
t1.update_taxon_namespace()
t1.update_bipartitions(
    suppress_unifurcations=False, suppress_storage=True
)  # suppress_storage is optional, I just do not want to create a bipartitions list
t1.print_plot()
str_t1 = t1.as_string(schema='newick')
print(str_t1)

NB！

更新taxa命名空间应该在更新bu分区之前，因为后者必须使用正确的TaxonNamespace。否则，你还是会有奇怪的行为。

然而，最好采用内建Node方法进行精细树的重建。例如，我会以这样的方式重写函数：

def insert_new_node_posterior(
    node: Node,
    *,
    taxon_label: Optional[str] = None,
    node_label: Optional[str] = None,
    edge_length: Real,
    # If it was product or at least reusable in the future code,
    # I would add more arguments for proportion specification,
    # using height, distance from root &c.
) -> Node:
    parent = node.parent_node
    if not parent:
        raise Exception("You cannot insert a node in posterior to the root.")

    new_taxon = Taxon(label=taxon_label)
    i = parent.child_nodes().index(node)
    parent.remove_child(node)
    intermediate_node = parent.insert_new_child(
        index=i, taxon=new_taxon, label=node_label, edge_length=edge_length
    )
    node.edge_length -= edge_length
    intermediate_node.add_child(node)
    return intermediate_node


node = insert_new_node_posterior(
    mrca,
    node_label="midway between root and MRCA sp4&sp5",
    edge_length=mrca.edge_length / 2
)
t1.update_taxon_namespace()
t1.update_bipartitions(
    suppress_unifurcations=False, suppress_storage=True
)

t1.print_plot()
str_t1 = t1.as_string(schema='newick')
print(str_t1)

尽管如此，Tree.mrca仍然显示了一个不正确的节点：

Node object at 0x1be8b959460<Node object at 0x1be8b959460: 'midway between root and MRCA sp4&sp5' (<Taxon 0x1be8cdceeb0 'None'>)>
    [Edge]
        Edge object at 0x1be8b959400 (1917897249792, Length=0.5)
    [Taxon]
         Taxon object at 0x1be8cdceeb0: <Unnamed Taxon>
    [Parent]
        Node object at 0x1be8c3b2b80<Node object at 0x1be8c3b2b80: 'root' (None)>
    [Children]
        [0] Node object at 0x1be8be4d6a0<Node object at 0x1be8be4d6a0: 'MRCA sp4&sp5' (None)>

不过，在这种情况下，这并不是一个bug，因为这只是方法的一个特性。由于这一点在源代码中

if cms:
    # for at least one taxon cm has 1 and bipartition has 1
    if cms == leafset_bitmask:
        # curr_node has all of the 1's that bipartition has
        if cm == leafset_bitmask:
            return curr_node  # Vovin's comment: Since there is a unifurcation,
                              # it returns the current node
                              # instead of the next iteration
        last_match = curr_node
        nd_source = iter(curr_node.child_nodes())
    else:
        # we have reached a child that has some, but not all of the
        #   required taxa as descendants, so we return the last_match
        return last_match

例如，如果我们将一个子节点添加到新节点中，那么它工作得很好：

node = insert_new_node_posterior(
    mrca,
    node_label="midway between root and MRCA sp4&sp5",
    edge_length=mrca.edge_length / 2
)
node.new_child(label="sp6", edge_length=1, taxon=Taxon(label="sp6"))
t1.update_taxon_namespace()
t1.update_bipartitions(
    suppress_unifurcations=False, suppress_storage=True
)
mrca = t1.mrca(taxon_labels=["sp4", "sp5"])
print(mrca.description())

Node object at 0x1be8c1e22b0<Node object at 0x1be8c1e22b0: 'MRCA sp4&sp5' (None)>
    [Edge]
        Edge object at 0x1be8c1e2340 (1917906199360, Length=0.5)
    [Taxon]
        None
    [Parent]
        Node object at 0x1be8ba8da30<Node object at 0x1be8ba8da30: 'midway between root and MRCA sp4&sp5' (<Taxon 0x1be8ba8d370 'None'>)>
    [Children]
        [0] Node object at 0x1be8c1e2910<Node object at 0x1be8c1e2910: 'None' (<Taxon 0x1be8c1e2640 'sp4'>)>
        [1] Node object at 0x1be8c1e28e0<Node object at 0x1be8c1e28e0: 'None' (<Taxon 0x1be8c1e2e50 'sp5'>)>