#!/usr/bin/env python3

from Bio import Entrez

""" 
Run elink using the history from a previous search.
"""

# Initial search, generates history parameters.
EQUERY="Fristensky [AUTH] AND Pisum [ORGN]"
h1 = Entrez.esearch(db="nuccore", term=EQUERY, usehistory="y", retmode="text", rettype="xml") 
result1= Entrez.read(h1)
h1.close()
WebEnv=result1["WebEnv"]
QueryKey=result1["QueryKey"]

# Use history from initial search to get an esummary
h2 = Entrez.esummary(db="nuccore", usehistory="y", WebEnv=WebEnv, query_key=QueryKey, retmode="text", rettype="xml") 
result2=Entrez.read(h2)
h2.close()
print(result2[0]["Id"])    

# Use history from initial search to get linked proteins
h3 = Entrez.elink(dbfrom="nuccore", db="protein", usehistory="y", WebEnv=WebEnv, query_key=QueryKey, retmode="xml", rettype="xml") 
lines = h3.readlines()

#outfile = open("testlink.xml","w")
# etree.ElementTree.fromstring needs XML  to be one long character string
XmlDoc=""
for l in lines :
#    outfile.write(l)
    XmlDoc = XmlDoc + l
#outfile.close()    

# lxml test
from xml import etree
tree = etree.ElementTree.fromstring(XmlDoc)
doc = tree.getroot()
print(doc)