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1 #!/usr/bin/env python
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2
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3 import sys, os
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4 import argparse
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5 import tempfile
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6 import readfile
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7 import rest_tool_functions
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8
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9
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10 #get the cids for bioassay aid
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11 def get_aid_cid_dict_for_list(aidlist):
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12 aidliststring=",".join(aidlist)
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13 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aidliststring+"/cids/xml"
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14 xml=readfile.getresult(url)
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15 tmp = tempfile.TemporaryFile()
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16 tmp.write(xml)
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17 tmp.seek(0)
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18 dic=rest_tool_functions.give_aid_cid_dict_from_xml(tmp)
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19 tmp.close()
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20 return dic
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21
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22 def main(args):
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23 if args.aid_file is None:
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24 aidlist=args.aid.split(",")
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25 else:
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26 aidlist=readfile.getListFromFile(args.aid_file)
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27 dic=get_aid_cid_dict_for_list(aidlist)
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28 rest_tool_functions.write_to_csv(dic, args.outfile)
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29
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30
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31 if __name__ == "__main__":
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32 parser = argparse.ArgumentParser()
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33 parser.add_argument('--aid', type=str,
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34 help="AIDs of the BioAssay")
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35 parser.add_argument('--aid-file', dest="aid_file", type=argparse.FileType('r'),
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36 help="Specify a file with a list of aids, one per line")
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37 parser.add_argument('--outfile', type=argparse.FileType('w'),
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38 help="Specify output file")
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39 if len(sys.argv) < 2:
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40 print "Too few arguments..."
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41 parser.print_help()
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42 exit(1)
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43 args = parser.parse_args()
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44 main( args )
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