Mercurial > repos > saket-choudhary > fathmm_web
comparison fathmm/fathmm.py @ 0:fd66648ce5f9 draft default tip
Uploaded
author | saket-choudhary |
---|---|
date | Tue, 07 Oct 2014 19:25:07 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-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) |