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1 #!/usr/bin/env python
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2 # Aufruf convert_graph.py --type type --operation op --id id --outformat format --outfile outfile
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3
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4 import sys, os
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5 import networkx as nx
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6 import argparse
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7 import urllib2
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8
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9 #supported graph_types
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10 output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"]
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11
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12
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13 def getresult(url):
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14 try:
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15 connection = urllib2.urlopen(url)
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16 except urllib2.HTTPError, e:
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17 return ""
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18 else:
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19 return connection.read().rstrip()
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20 def main(args):
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21 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
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22 if args.type == "assay":
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23 url+="aid/"
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24 elif args.type == "compound":
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25 url+="cid/"
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26 url+=args.id+"/"+args.operation+"/"+args.outformat
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27 print(url)
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28 print(args.type)
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29 data=getresult(url)
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30 file=args.outfile
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31 file.write(data)
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32 file.close()
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33
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34 if __name__ == "__main__":
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35 parser = argparse.ArgumentParser()
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36 parser.add_argument('--type', type=str,
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37 help="That you want BioAssay Compund ...")
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38 parser.add_argument('--id', type=str,
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39 help="Specify the ID")
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40 parser.add_argument('--operation', type=str,
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41 help="Specify the operation")
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42 parser.add_argument('--property-value', type=str,
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43 help="Specify the property")
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44 parser.add_argument('--outformat', type=str,
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45 help="Specify the format of the output", choices = output_types)
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46 parser.add_argument('--outfile', type=argparse.FileType('w'),
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47 help="Specify one output file")
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48 if len(sys.argv) < 8:
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49 print "Too few arguments..."
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50 parser.print_help()
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51 exit(1)
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52 args = parser.parse_args()
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53 main( args )
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