Installing ete2 is not entirely straightforward, but it is described at http://etetoolkit.org/download/.
This tutorial requires installing th PyQT4 dependency for the tree vis steps.
Installing Peyotl is straightforward and is described here http://opentreeoflife.github.io/peyotl/installation/



In [1]:

    
import peyotl
from ete2 import Tree, TreeStyle

These functions use peyotl wrappers around OpenTree API calls, described at https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs



In [2]:

    
def ot_find_tree(pair, exact=True,  verbose=False, oti_wrapper=None):          
    '''Uses a peyotl wrapper around an Open Tree web service to get a list of trees including 
    values `value` for a given property to be searched on `property`.
    The oti_wrapper can be None (in which case the default wrapper from peyotl.sugar will be used.
    All other arguments correspond to the arguments of the web-service call.
    '''
    if oti_wrapper is None:
        from peyotl.sugar import oti
        oti_wrapper = oti
    match_obj = oti_wrapper.find_trees(pair, exact=exact, verbose=verbose)
    return match_obj



In [3]:

    
def ot_get_tree(study_id, tree_id,**kwargs):
    from peyotl.api import APIWrapper
    api_wrapper = APIWrapper()
    if 'format' in kwargs:
        match_obj = api_wrapper.study.get(study_id,tree=tree_id,format=kwargs['format'])
    else:
        match_obj = api_wrapper.study.get(study_id,tree=tree_id)
    return match_obj

Changing the values here can allow you select trees with any values in trees' searchable properties.
Properties include: "is_deprecated", "ot:treebaseTreeId", "ot:branchLengthMode", "ot:comment", "ot:branchLengthDescription", "ot:nodeLabelMode", "ot:originalLabel", "ot:studyId", "ot:ottId", "ot:treeModified", "ot:treebaseOTUId", "ot:tag", "ot:treeLastEdited", "ot:inferenceMethod", "ot:ottTaxonName", "ot:branchLengthTimeUnits", "ot:nodeLabelDescription", "oti_tree_id"



In [4]:

    
arg_dict = {"ot:ottTaxonName": "Apis mellifera"}



In [5]:

    
tree_list = ot_find_tree(arg_dict)



In [6]:

    
for study in tree_list:
  for tree in study['matched_trees']:
   study_id=study['ot:studyId']
   for tree in study['matched_trees']:
            tnew=ot_get_tree(study_id, tree['oti_tree_id'],format='newick')
            t = Tree(tnew, format=1)
            if len(t) < 100:#this is just an aribitrary way to grab a tree isn't too hard to visualize
                break

Using ETE you can visualize the trees pulled down from the OpenTree database in an ipython notebook!



In [7]:

    
circular_style = TreeStyle()
circular_style.mode = "c" # draw tree in circular mode
circular_style.scale = 30
t.render("%%inline", units="mm", tree_style=circular_style)









    Out[7]:



In [8]:

    
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 180
ts.scale = 40
t.render("%%inline", units='mm', tree_style=ts)









    Out[8]:



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