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1 #!/usr/bin/env python
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2 import sys
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3 import requests
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4 import os
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5 import argparse
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6 import re
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7
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8 __url__ = 'http://mutationassessor.org/'
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9
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10
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11 def stop_err(msg, err=1):
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12 sys.stderr.write('%s\n' % msg)
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13 sys.exit(err)
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14
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15
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16 def main_web(args):
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17 assert os.path.exists(args.input)
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18 with open(args.input) as f:
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19 contents = f.read().strip()
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20 if args.hg19 is True and args.protein is True:
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21 stop_err('--hg19 option conflicts with --protein')
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22 if args.protein is False:
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23 ## Replace tabs/space with commas
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24 re.sub('[\t\s]+', ',', contents)
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25 if args.hg19:
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26 ## Append hg19 to each line
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27 lines = contents.split('\n')
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28 contents = ('\n').join(
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29 map((lambda x: 'hg19,' + x),
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30 lines))
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31
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32 payload = {'vars': contents, 'tableQ': 1}
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33 request = requests.post(__url__, data=payload)
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34 response = request.text
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35 if request.status_code != requests.codes.ok:
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36 stop_err("""Error retrieving response from server.
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37 Server returned %s .
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38 Output: %s
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39 """ % (request.status_code, response))
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40 with open(args.output, 'wb') as fp:
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41 fp.write(response)
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42
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43 if __name__ == '__main__':
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44 parser = argparse.ArgumentParser(description="Process input output paths")
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45 parser.add_argument('--input',
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46 type=str,
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47 required=True,
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48 help='Input file location')
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49 parser.add_argument('--output',
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50 type=str,
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51 required=True,
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52 help='Output file locatio')
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53 parser.add_argument('--log',
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54 type=str,
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55 required=False)
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56 parser.add_argument('--hg19',
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57 action='store_true',
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58 help="""Use hg19 build.
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59 Appends 'hg19' to each input line""")
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60 parser.add_argument('--protein',
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61 action='store_true',
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62 help='Inputs are in protein space')
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63 args = parser.parse_args()
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64 main_web(args)
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