Question

Alright,
I have this program to sparse code in Newick Format, which extracts both a name, and a distance for use in a phylogenetic tree diagram.
What my problem is, in this branch of code, as the program reads through the newickNode function, it assigns the name and distance to the ‘node’ variable, then returns it back into the ‘Node’ class to be printed, but it seems to only print the first node ‘A’, and skips the other 3.
Is there anyway to finish the for loop in newickNode to read the other 3 nodes and print them accordingly with the first?

class Node:
    def __init__(self, name, distance, parent=None):
        self.name = name
        self.distance = distance
        self.children = []  
        self.parent = parent

    def displayNode(self):
        print "Name:",self.name,",Distance:",self.distance,",Children:",self.children,",Parent:",self.parent

def newickNode(newickString, parent=None):
    String = newickString[1:-1].split(',')
    for x in String:
        splitString = x.split(':')
        nodeName = splitString[0]
        nodeDistance = float(splitString[1]) 
        node = Node(nodeName, nodeDistance, parent)
        return node

Node1 = newickNode('(A:0.1,B:0.2,C:0.3,D:0.4)')
Node1.displayNode()

Thanks!

Answer 1

You could make it a generator:

def newickNode(newickString, parent=None):
    String = newickString[1:-1].split(',')
    for x in String:
        splitString = x.split(':')
        nodeName = splitString[0]
        nodeDistance = float(splitString[1]) 
        node = Node(nodeName, nodeDistance, parent)
        yield node

for node in newickNode('(A:0.1,B:0.2,C:0.3,D:0.4)'): 
    node.displayNode()

The generator will return one node at a time and pause within the function, and then resume when you want the next one.

Or just save them up and return them

def newickNode(newickString, parent=None):
    String = newickString[1:-1].split(',')
    nodes = []
    for x in String:
        splitString = x.split(':')
        nodeName = splitString[0]
        nodeDistance = float(splitString[1]) 
        node = Node(nodeName, nodeDistance, parent)
        nodes.append(node)
    return nodes