Adding new nodes to a Tree

[hsa...@cs.stonybrook.edu]

I would like to create a tree by dynamically adding nodes to an already existing tree in DendroPy. So here is how I am proceeding,

>>>t1 = dendropy.Tree(stream=StringIO("(8,3)"),schema="newick")

Now That creates a small tree with two children having Taxon labels 8 and 3. Now I want to add a new leaf to the node with taxon label 3. In order to do that I want the node object.

>>>cp = t1.find_node_with_taxon_label('3')

I want to use add child function at that point which is an attribute of a node.

>>>n = dendropy.Node(taxon='5',label='5')
>>>cp.add_child(n)

But even after adding the node when I am printing all the node objects in t1, It is returning the only children 8 and 3 that it was initialized with. Please help me to understand how to add nodes in an existing tree in dendropy..

[Sourya Bhattacharyya]

In addition, you may use the following statement:

n.parent_node = cp

This will explicitly set the parent information of the node n

Then you apply 

t1.update_splits()

and check whether the tree t1 has the new taxon information.

Please notify whether it works.

[Jeet Sukumaran]

Both approaches work fine:

~~~
import dendropy

t1 = dendropy.Tree.get(
data="(8,3);",
schema="newick")

cp = t1.find_node_with_taxon_label("3")

n1 = dendropy.Node(taxon=t1.taxon_namespace.require_taxon(label="5"))
cp.add_child(n1)
n2 = dendropy.Node(taxon=t1.taxon_namespace.require_taxon(label="6"))
cp.add_child(n2)
print(t1.as_string(schema="newick"))
~~

or

~~
import dendropy

t1 = dendropy.Tree.get(
data="(8,3);",
schema="newick")

cp = t1.find_node_with_taxon_label("3")

n1 = dendropy.Node(taxon=t1.taxon_namespace.require_taxon(label="5"))
n1.parent_node = cp
n2 = dendropy.Node(taxon=t1.taxon_namespace.require_taxon(label="6"))
n2.parent_node = cp
print(t1.as_string(schema="newick"))
~~

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