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1 #!/usr/bin/env python
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2
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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 import urllib2, urllib, httplib
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7 import readfile
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8 import xml.sax as sax
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9
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10 class DictHandler(sax.handler.ContentHandler):
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11
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12 def __init__(self):
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13 self.ergebnis = {}
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14 self.schluessel = ""
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15 self.wert = ""
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16 self.aktiv = None
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17
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18 def startElement(self, name, attrs):
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19 if name == "Information":
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20 self.schluessel = ""
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21 self.wert = ""
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22 elif name == "AID" or name=="CID":
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23 self.aktiv = name
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24
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25 def endElement(self, name):
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26 if name == "AID":
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27 self.schluessel=self.schluessel.strip()
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28 self.ergebnis[self.schluessel]=[]
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29 #print("huhn")
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30 self.aktiv=None
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31 elif name == "CID":
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32 self.aktiv = None
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33 self.ergebnis[self.schluessel].append(self.wert)
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34 self.wert=""
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35 def characters(self, content):
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36 if self.aktiv == "AID":
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37 self.schluessel += content
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38 elif self.aktiv == "CID":
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39 self.wert += content
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40
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41
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42 def give_aid_cid_dict_from_xml(xmlfile):
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43 handler = DictHandler()
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44 parser = sax.make_parser()
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45 parser.setContentHandler(handler)
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46 parser.parse(xmlfile)
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47 dic=handler.ergebnis
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48 return dic
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49
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50 #get every aid as a list
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51 #returns a dictionary with aid as key and as value the list of cids
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52 def getAllAssayIDs():
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53 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/type/all/aids/TXT"
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54 data=readfile.getresult(url)
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55 aidlist=readfile.getListFromString(data)
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56 return aidlist
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57
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58
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59 def getIDofLine(line):
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60 arr=line.split(">")
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61 if len(arr) > 1:
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62 aid=arr[1].split("<")[0]
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63 return aid
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64 else:
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65 return "-1"
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66
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67 def write_to_csv(aid_cid_dict, outfile):
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68 for key in aid_cid_dict:
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69 for cid in aid_cid_dict[key]:
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70 outfile.write(key)
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71 outfile.write(",")
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72 outfile.write(cid)
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73 outfile.write("\n")
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74
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