Getting information on trees that intersect with a clade of interest

Hopefully you have peyotl installed and if not check this out. So I assume that you have a working peyotl and you understand virtualenv (if you use it).

##Getting information on studies with taxa of interest## Put this in a file

from peyotl.api import APIWrapper
a = APIWrapper()
oti = a.oti
b = oti.find_trees(ottTaxonName='Lonicera')

You will get a list of studies that include the taxon Lonicera. If you wanted to search by ottId instead, you simply would change the line to b = oti.find_trees(ottId=649885). b will be a list that includes the relevant study ids and for each study, the relevant tree ids. To see that list, you can just add to the file that you have these lines

for i in b:
    print i['ot:studyId']

which will produce

pg_424
pg_422

and then you can get the tree ids with this

for i in b:
    for j in i['matched_trees']:
        print j['oti_tree_id']

which will produce

pg_424_tree532
pg_422_tree531

You can check out these studies on the curator here pg_424 and pg_422. We are going to look at downloading the files associated with these in the next tutorial.

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