Phylo example

"""
A simple script illustraing how to generate a CSV for Anki to learn phylogenies
"""

import requests
import io
import xml.etree.ElementTree as ET
import csv

file = io.BytesIO(requests.get("http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=70802").content)
tree = ET.parse(file)

def relations(tree):
    '''returns collection of relationships from tree''' 
    
    # get root of tree
    root = tree.getroot().find("NODE")
    
    # dictionary to track relationships 
    relationships = {"Parent-Child": [], "Child-Parent": []}
      
    def subtree_relations(parent_name, root, relationships): 
        '''function to recurse on tree'''

        # name of root node 
        name = root.find("NAME").text

        # add relationship of root node to parent
        if parent_name is not None:
            relationships["Child-Parent"].append( [name, parent_name] )
                
        if root.find("NODES") is None:
            return 
        
        # children of root node
        children = [child for child in root.find("NODES").getchildren() if child.find("NAME").text is not None] 
                        
        # add parent-child relationships
        relationships["Parent-Child"].append( [name, [child.find("NAME").text for child in children]] )
        
        # recurse on tree
        for child in children:
            subtree_relations(name, child, relationships)
    
    # start recursion    
    subtree_relations(None, root, relationships)
    
    return relationships
    
    
   rels = relations(tree)

with open("out.csv", "w") as f:
    writer = csv.writer(f)
    # column names
    writer.writerow(["Field 1", "Field 2", "Relationship Type"])
    
    for rel in rels["Parent-Child"]:
        row = [rel[0], ", ".join(rel[1]), "Parent-Child"]
        writer.writerow(row)
    
    for rel in rels["Child-Parent"]:
        writer.writerow(rel + ["Child-Parent"])