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ponzi.py
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ponzi.py
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#!/usr/bin/env python
"""
ponzi.py
Ryan Bressler, Institute for Systems Biology
Webservice for doing hypergeometric testing against gene sets in a gmt file from the broad:
http://www.broadinstitute.org/gsea/downloads.jsp
Commanly used with kegg pathways:
http://www.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/4.0/c2.cp.kegg.v4.0.symbols.gmt
Start As a tornado webservice Service on port 8000:
ponzi.py 8000 pathwaydb.gmt
See README.md for API.
"""
import json
import numpy as np
import sys
from scipy.stats import hypergeom
import tornado.ioloop
import tornado.web
import tornado.escape
def startTornado(port,dbfilename):
#load needed data into memory
pathways = []
defaultbackground = []
gmtDB = open(dbfilename)
for line in gmtDB:
vs=line.rstrip().split("\t")
setgenes=np.array(vs[2:])
pathways.append({"name":vs[0],"link":vs[1],"genes":setgenes})
defaultbackground.extend(setgenes)
gmtDB.close()
defaultbackground = np.unique(defaultbackground)
#this is in here so that the handler is a closure using the
#local variables holding the pathway and background data
class MainHandler(tornado.web.RequestHandler):
def post(self):
background = defaultbackground
try:
args = tornado.escape.json_decode(self.request.body)
except ValueError:
self.clear()
self.set_status(400)
self.finish("<html><head><title>400 Bad Request</title></head><body>Malformed JSON object in POST body.</body></html>")
if "background" in args and len(args["background"])!=0:
background = np.unique(args["background"])
total= len(background)
replydata = {}
for setname in args["lists"]:
genes = np.unique(args["lists"][setname])
ntrys = len(genes)
names =[]
links =[]
probs =[]
for pathway in pathways:
setgenes=pathway["genes"]
nfound = np.sum(np.in1d(genes,setgenes,assume_unique=True))
if nfound > 1:
npresent = np.sum(np.in1d(setgenes,background,assume_unique=True))
prob = hypergeom.sf(nfound-1,total,npresent,ntrys)
names.append(pathway["name"])
links.append(pathway["link"])
probs.append(prob)
sortedarray = []
#for i in np.argsort(np.array(probs))[0:returnn]:
for i in np.argsort(np.array(probs)):
sortedarray.append({"name":names[i],"link":links[i],"p":probs[i]})
replydata[setname]=sortedarray
json.dump({'results': replydata}, self)
application = tornado.web.Application([
(r"/", MainHandler),
])
application.listen(port)
tornado.ioloop.IOLoop.instance().start()
def main():
if len(sys.argv) == 3:
startTornado(sys.argv[1],sys.argv[2])
else:
print '''Comand line usage:
hypergeom.py genes.txt backgroundgenes.txt pathwaydb.gmt
Start As a tornado webservice Service on port 8000:
hypergeom.py 8000 pathwaydb.gmt'''
if __name__ == '__main__':
main()