Python For...loop iteration

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!

jdi · Accepted Answer · 2012-06-25 18:52:36Z

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

kindall · Accepted Answer · 2012-06-25 19:40:27Z

Your newickNode() function should accumulate a list of nodes and return that, rather than returning the first node created. If you're going to do that, why have a loop to begin with?

def newickNodes(newickString, parent=None):
    nodes = []
    for node in newickString[1:-1].split(','):
        nodeName, nodeDistance = node.split(':')
        nodes.append(Node(nodeName, nodeDistance, parent))
    return nodes

Alternatively, you could write it as a generator that yields the nodes one at a time. This would allow you to easily iterate over them or convert them to a list depending on your needs.

def newickNodes(newickString, parent=None):
    for node in newickString[1:-1].split(','):
        nodeName, nodeDistance = node.split(':')
        yield Node(nodeName, nodeDistance, parent)

Also, from a object-oriented design POV, this should probably be a class method on your Node class named parseNewickString() or similar.

Daniel Roseman · Accepted Answer · 2012-06-25 18:52:11Z

1

Alternatively, your newickNode() function could immediately call node.displayNode() on the new node each time through the loop.

answered Jun 25, 2012 at 18:52

Daniel Roseman

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1 Comment

Sean Over a year ago

wow thank you, idk why i didnt see that before, my code was as simple as such as i was able to breakdown and parse the string using another func. i had in my code.

Jon Clements · Accepted Answer · 2012-06-25 19:07:14Z

1

To keep this more flexible - I would use pyparsing to process the Newick text and networkx so I had all the graph functionality I could desire - recommend to easy_install/pip those modules. It's also nice that someone has written a parser with node and tree creation already (although it looks like it lacks some features, it'll work for your case):

http://code.google.com/p/phylopy/source/browse/trunk/src/phylopy/newick.py?r=66

answered Jun 25, 2012 at 19:07

Jon Clements

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Comments

Wooble · Accepted Answer · 2012-06-25 18:51:30Z

0

The first time through your for: loop, you return a node, which stops the function executing.

If you want to return a list of nodes, create the list at the top of the function, append to it each time through the loop, and return the list when you're done.

It may make more sense to move the loop outside of the newickNode function, and have that function only return a single node as its name suggests.

answered Jun 25, 2012 at 18:51

Wooble

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