treemachine wrapper

NOTE see the comments about the two styles of wrappers on the API wrappers page.

Treemachine

Treemachine is a neo4j application that provides the web-services (TNRS and data access) around working the open tree synthetic tree and the graph of life from well-curated published trees. In v2 of the Open Tree API, treemachine provides provides the [domains]/tree_of_life/* and the the [domains]/tree_of_life/* methods.

The code examples below assume that you have an instance of the wrapper via something like:

#!/usr/bin/env
from peyotl.api import APIWrapper
tm = APIWrapper().treemachine
tax = APIWrapper().taxomachine
# Get info about synthesis
info = tm.get_synthetic_tree_info()
# Get tree ID
tid = info['tree_id']
# Get the OTT IDs from taxomachine
human, gorilla = tax.names_to_ott_ids_perfect(['homo sapiens', 'Gorilla gorilla'])
mrca_info = tm.mrca(ott_ids=[human, gorilla])
mrca_node_id = mrca_info['mrca_node_id']
# fetch a few levels of the tree:
newick = tm.get_synthetic_tree(tid, format="newick", node_id=mrca_node_id)['newick']
# pruned is silly for just 2 leaves, but...
newick = tm.get_synth_tree_pruned(ott_ids=[human, gorilla])['subtree']
# Get list of dicts describing the version of each input tree
inputs = tm.get_synthetic_tree_id_list()

shared-API wrapper-style

from peyotl.api import APIWrapper
tol = APIWrapper().tree_of_life
# Get info about synthesis
info = tol.about()
# Get list of dicts describing the version of each input tree
tol.about()['study_list']
# Get tree ID
tid = info['tree_id']
# Get root node ID
nid = info['root_node_id']
# fetch a few levels of the tree:
newick = tm.get_synthetic_tree(tid, format="newick", node_id=nid, max_depth=2)
  • taxo.valid_contexts read-only property of the set of names that can be used as “context” to narrow the name searching.

  • taxo.TNRS(["name 1", "name 2"...], context) returns a list of TNRS results for each of the names passed in.

    from peyotl.api import APIWrapper oti = APIWrapper().oti