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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
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6 import readfile
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7
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8 txt_output=["cids", "aids", "sids", "synonyms" ]
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9 csv_output=["assaysummary"]
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10 check_for_id_type=["cids", "aids", "sids"]
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11
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12 def main(args):
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13 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
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14 if args.type == "assay":
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15 url+="aid/"
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16 elif args.type == "compound":
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17 url+="cid/"
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18 elif args.type == "substance":
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19 url+="sid/"
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20 if args.id_file is None:
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21 idstring=str(args.id)
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22 else:
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23 idlist=readfile.getListFromFile(args.id_file)
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24 idstring=",".join(idlist)
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25 url+=idstring+"/"+args.operation+"/"
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26 if args.operation in csv_output:
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27 url+="csv"
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28 elif args.operation in txt_output:
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29 url+="txt"
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30 else:
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31 url+="xml"
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32 if args.operation in check_for_id_type and not args.id_type is None:
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33 url+="?"+args.operation+"_type="+args.id_type
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34 print(url)
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35 data=readfile.getresult(url)
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36 outfile=args.outfile
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37 outfile.write(data)
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38 outfile.close()
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39
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40 if __name__ == "__main__":
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41 parser = argparse.ArgumentParser()
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42 parser.add_argument('--type', type=str, required=True,
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43 help="That you want BioAssay Compund ...")
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44 parser.add_argument('--id', type=str,
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45 help="Specify the ID")
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46 parser.add_argument('--operation', type=str, required=True,
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47 help="Specify the operation")
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48 parser.add_argument('--property-value', dest="property_value", type=str,
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49 help="Specify the property")
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50 parser.add_argument('--id-type', dest="id_type", type=str,
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51 help="Specify the property")
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52 parser.add_argument('--outfile', type=argparse.FileType('w'), required=True,
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53 help="Specify one output file")
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54 parser.add_argument('--id-file', dest="id_file", type=argparse.FileType('r'),
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55 help="Specify a file with a list of ids, one per line")
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56 if len(sys.argv) < 8:
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57 print "Too few arguments..."
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58 parser.print_help()
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59 exit(1)
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60 args = parser.parse_args()
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61 main( args )
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