Using Treebase
==============

``ivy`` has functions to pull trees from `Treebase <http://treebase.org/treebase-web/about.html;jsessionid=5B7D6A265E17EFAB9565327D3A78CD4B>`_.


Fetching the study
------------------

If you have an id for a study on treebase, you can fetch the study and
access the trees contained within the study.

.. sourcecode:: ipython

    In [*]: import ivy
    In [*]: from ivy.treebase import fetch_study
    In [*]: study_id = "1411" # The leafy cactus genus Pereskia
    In [*]: e = fetch_study(study_id, 'nexml') # e is an lxml etree


Accessing the tree
------------------

You can parse the output of fetch_study using the parse_nexml function,
 then access the tree(s) contained within the study.

.. sourcecode:: ipython

    In [*]: from ivy.treebase import parse_nexml
    In [*]: x = parse_nexml(e) # x is an ivy Storage object
    In [*]: r = x.trees[0].root
    In [*]: from ivy.interactive import treefig
    In [*]: fig = treefig(r)