AMELIE API query from command line inputs

amelie.py

#! /usr/bin/env python2

# $1 gene list
# $2 HPO term list

import urllib3
import requests
import json
import sys
import os

# open gene list
with open(sys.argv[1],'r') as genelist:
	genes = genelist.read().splitlines()

ameliegenes = ','.join(genes)

print('You gave these genes:')
print(ameliegenes + '\n')

# open hpo list
with open(sys.argv[2],'r') as phenotypelist:
    phenotypes = phenotypelist.read().splitlines()

ameliephenotypes = ','.join(phenotypes)

print('You gave these phenotypes:')
print(ameliephenotypes + '\n')

requests.packages.urllib3.disable_warnings() 
response = requests.post('https://amelie.stanford.edu/api/', verify=False, data={'genes':ameliegenes,'phenotypes':ameliephenotypes})
responses = json.loads(response.text)

print('AMELIE gave this output:')
for out in responses:
    gene = out[0]
    result = []
    for li in out[1:]:
       result.extend("score:%.3f, pmid:%s" % tuple(v) for v in li)
    print(gene + "\t" + "\t".join(result))

Usage: python amelie.py genelist.txt hpolist.txt