#!/usr/bin/env python import sys import os from treestore import Treestore try: taxonomy = sys.argv[1] except: taxonomy = None t = Treestore() treebase_uri = 'http://purl.org/phylo/treebase/phylows/tree/%s' tree_files = [x for x in os.listdir('trees') if x.endswith('.nex')] base_uri = 'http://www.phylocommons.org/trees/%s' tree_list = set(t.list_trees()) for tree_uri in tree_list: if not 'TB2_' in tree_uri: continue tree_id = t.id_from_uri(tree_uri) tb_uri = treebase_uri % (tree_id.replace('_', ':')) print tree_id, tb_uri t.annotate(tree_uri, annotations='?tree bibo:cites <%s> .' % tb_uri)
def tree_id_from_uri(uri): return Treestore.id_from_uri(uri, base_uri=settings.TREE_URI)