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1 #!/usr/bin/env python
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2 # Aufruf convert_graph.py --aid list of ids --aid-from-file file
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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, urllib, httplib
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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
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21
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22 def getresultPost(url, aidList):
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23 values={'aids': ",".join(aidList)}
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24 data=urllib.urlencode(values)
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25 print(data)
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26
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27 headers = {"Content-type": "application/x-www-form-urlencoded"}
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28 conn = httplib.HTTPConnection("pubchem.ncbi.nlm.nih.gov")
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29 conn.request("POST", "/rest/pug/assay/aid/aids/csv", data, headers)
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30 response = conn.getresponse()
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31 conn.close()
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32 return response.read()
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33
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34
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35
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36 #get the cids for bioassay aid
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37 def getCompoundList(aid):
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38 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aid+"/cids/txt"
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39 data=getresult(url)
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40 return data
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41
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42 def main(args):
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43 cids=getCompoundList(args.aid)
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44 args.outfile.write(cids)
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45 args.outfile.close()
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46 if __name__ == "__main__":
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47 parser = argparse.ArgumentParser()
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48 parser.add_argument('--aid', type=str,
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49 help="AIDs of the BioAssay")
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50 parser.add_argument('--aid-from-file', type=argparse.FileType('r'),
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51 help="Specify a file with a list of aids, one per line")
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52 parser.add_argument('--outfile', type=argparse.FileType('w'),
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53 help="Specify output file")
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54 if len(sys.argv) < 2:
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55 print "Too few arguments..."
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56 parser.print_help()
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57 exit(1)
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58 args = parser.parse_args()
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59 main( args )
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