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1 #!/usr/bin/env python
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2 # Aufruf convert_graph.py --type type --operation op --id id --outfile outfile
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3
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4 import sys, os
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5 import argparse
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6
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7 import readfile
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8
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9 txt_output=["cids", "summary", "synonyms" ]
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10
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11 def main(args):
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12 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
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13 if args.type == "assay":
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14 url+="aid/"
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15 elif args.type == "compound":
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16 url+="cid/"
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17 elif args.type == "substance":
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18 url+="sid/"
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19 if args.idfile is None:
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20 idstring=str(args.id)
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21 else:
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22 idlist=readfile.getListFromFile(args.idfile)
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23 idstring=",".join(idlist)
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24 url+=idstring+"/"+args.operation+"/"
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25 if args.operation in txt_output:
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26 url+="txt"
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27 else:
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28 url+="csv"
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29 print(url)
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30 data=readfile.getresult(url)
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31 outfile=args.outfile
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32 outfile.write(data)
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33 outfile.close()
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34
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35 if __name__ == "__main__":
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36 parser = argparse.ArgumentParser()
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37 parser.add_argument('--type', type=str,
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38 help="That you want BioAssay Compund ...")
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39 parser.add_argument('--id', type=str,
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40 help="Specify the ID")
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41 parser.add_argument('--operation', type=str,
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42 help="Specify the operation")
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43 parser.add_argument('--property-value', type=str,
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44 help="Specify the property")
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45 parser.add_argument('--outfile', type=argparse.FileType('w'),
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46 help="Specify one output file")
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47 parser.add_argument('--idfile', type=argparse.FileType('r'),
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48 help="Specify a file with a list of ids, one per line")
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49 if len(sys.argv) < 8:
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50 print "Too few arguments..."
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51 parser.print_help()
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52 exit(1)
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53 args = parser.parse_args()
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54 main( args )
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