Mercurial > repos > saket-choudhary > fathmm_web

comparison fathmm/fathmm.py @ 0:fd66648ce5f9 draft default tip

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author saket-choudhary
date Tue, 07 Oct 2014 19:25:07 -0400
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-1:000000000000 0:fd66648ce5f9
1 import requests
2 import argparse
3 import os
4 import sys
5
6 __base_url__ = "http://supfam3.cs.bris.ac.uk/FATHMM/"
7 __submit_url__ = __base_url__ + "cgi-bin/submit.cgi"
8 __result_url__ = __base_url__ + "cgi-bin/"
9 __download_url__ = __base_url__ + "tmp/"
10 __type__="CANCER" ##Hidden field to show which type of variants we are processing
11
12
13 def stop_err(msg, err=1):
14 sys.stderr.write('%s\n' % msg)
15 sys.exit(err)
16
17 def main_web(args):
18 assert os.path.exists(args.input)
19 with open(args.input) as f:
20 contents = f.read().strip()
21 threshold = -0.75
22 if (args.threshold):
23 threshold = float(args.threshold)
24 data = {"weighted": __type__,
25 "batch": contents,
26 "threshold": threshold
27 }
28 response = requests.post(__submit_url__, data=data)
29 if response.status_code!=200:
30 stop_err("Error processing request, got" + response.status_code)
31 text = response.text
32 split_text = text.split("window.location = ")
33 try:
34 url = split_text[1]
35 url = url.split(";")[0]
36 url = url.split("session=")[1]
37 url = url.replace("'", "").replace("./","")
38 url = __download_url__ + url + ".tab"
39 except IndexError:
40 stop_err("Unable to parse result id")
41 response = requests.get(url)
42 with open(args.output, 'wb') as fp:
43 fp.write(response.text)
44
45 if __name__ == '__main__':
46 parser = argparse.ArgumentParser(description="Process input output paths")
47 parser.add_argument('--input',
48 type=str,
49 required=True,
50 help='Input file location')
51 parser.add_argument('--output',
52 type=str,
53 required=True,
54 help='Output file location')
55 parser.add_argument('--threshold',
56 type=float,
57 required=False,
58 help='Predictions with score less than threshold are possibly cancer causing')
59 args = parser.parse_args()
60 main_web(args)