#treeid = "ENSGT00390000013823"
server = "http://beta.rest.ensembl.org"
ext = "/genetree/id/" + treeid + "?"
resp, content = http.request(server+ext, method="GET", headers={"Content-Type":"application/json"})
if not resp.status == 200:
print "Invalid response: ", resp.status
continue #evil continue
decoded = json.loads(content)
tree = decoded['tree']
geneNodeMap = {}
root = TreeNode()
visit_json_elem(tree, root, geneNodeMap)
orthologs = set()
paralogs = set()
paralogs_dubious = set()
for g1 in geneNodeMap:
for g2 in geneNodeMap:
if g1 != g2:
n1 = geneNodeMap[g1]
n2 = geneNodeMap[g2]
lca = n1.get_common_ancestor(n2)
if lca.name == 'duplication' or lca.name == 'gene_split':
##################################
ass_node2parent = {"1": "1"}
for nodeid in taxa:
parentid = node2parent[nodeid]
while nodeid != parentid: #costruiamo un nuovo dizionario per i soli taxa che abbiamo identificato nel campione
ass_node2parent[nodeid] = parentid
nodeid = parentid
parentid = node2parent[nodeid]
node2parentid = {}
for nodeid in ass_node2parent.keys():
parentid = ass_node2parent[nodeid]
# Stores node connections
all_ids.update([nodeid, parentid])
# Creates a new TreeNode instance for each new node in file
n = TreeNode()
# Sets some TreeNode attributes
n.add_feature("name", node2name[nodeid])
n.add_feature("taxid", nodeid)
n.add_feature("Order", node2order[nodeid])
# updates node list and connections
node2parentid[n] = parentid
id2node[nodeid] = n
print len(id2node)
# Reconstruct tree topology from previously stored tree connections
print 'Reconstructing tree topology...'
for node in id2node.itervalues():
parentid = node2parentid[node]
parent = id2node[parentid]
# node with taxid=1 is the root of the tree
