by Open Tree of Life developers (primarily Mark T. Holder, Emily Jane McTavish, Duke Leto, and Jim Allman)
Big Thanks to NSF!
...org/treemachine/
v1/getDraftTree...
peyotl
api wrapperspeyotl
interface won't (hopefully)from peyotl.sugar import taxomachine print taxomachine.TNRS('Anolis sagrei')
returns a object summarizing the possible matches.
from peyotl.sugar import treemachine as tm o = [515698, 515712, 149491, 876340, 505091, 840022, 692350, 451182, 301424, 876348, 515698, 1045579, 267484, 128308, 380453, 678579, 883864, 863991, 3898562, 23821, 673540, 122251, 106729, 1084532, 541659] r = tm.get_synth_tree_pruned(ott_ids=o)
returns the tree (currently only in an odd, in-house format called "Arguson")
from peyotl.sugar import oti n = 'Aponogeoton ulvaceus' print oti.find_trees(ottTaxonName=n)
returns a list of objects listing studyID and treeID
from peyotl.api import PhylesystemAPI pa = PhylesystemAPI(get_from='api') print pa.get('pg_10', tree_id='tree3', subtree_id='ingroup', format='newick')returns the ingroup of "tree3¨ from study "pg_10" in newick.
pa = PhylesystemAPI(get_from='api', transform='server')
pa = PhylesystemAPI(get_from='api', transform='client')
pa = PhylesystemAPI(get_from='external')
pa = PhylesystemAPI(get_from='local')
t = pa.get('pg_10',...
request tree
look up location of study NexSON file
read NexSON file
extract tree
convert to newick
return to client
request tree
look up location of study NexSON file
read NexSON file
return to client
extract tree
convert to newick
request tree
look up GitHub URL of study NexSON file
return to study NexSON client
extract tree
convert to newick
request tree
look up location of study NexSON file
read NexSON file
extract tree
convert to newick
In the phylesystem-API
:
the datastore is publicly accessible as the git repo (Emily Jane McTavish's talk)
the library (peyotl
) adding functionality to the data was designed to be a server-side and a client-side library.
I'm hoping that peyotl
will be:
a useful tool for Python programmers,
a easy-to-grok entry point to the intimidating set of services offered by the Open Tree of Life effort.
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