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