comparison rest_tool_assays_with_cids_given_target.py @ 6:9ee84d9fd3a7 draft

Uploaded

6:9ee84d9fd3a7

#!/usr/bin/env python


import sys, os
import argparse
import readfile

#get every aid as a list
#returns a dictionary with aid as key and as value the list of cids
def getAllAssayIDs():
    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/type/all/aids/TXT"
    data=readfile.getresult(url)
    aidlist=readfile.getListFromString(data)
    return aidlist


def getIDofLine(line):
    arr=line.split(">")
    if len(arr) > 1:
        aid=arr[1].split("<")[0]
        return aid
    else:
        return "-1"
        
#get xml of all aids with cids for an activity
def getAllCidsForAssayActivity(activity):
    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/activity/"+activity+"/aids/txt?list_return=listkey"
    listkey=readfile.getresult(url)
#    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/listkey/"+listkey+"/cids/xml"
    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/25425,12345/cids/xml"
    print("url: "+url)
    xml=readfile.getresult(url)
    
    #init parser
    handler = DictHandler() 
    parser = sax.make_parser() 
    parser.setContentHandler(handler) 

    tempfile=open("tempfile","w")
    #handle the last line, there is sometimes some random output
    lastline_arr=xml.split("\n")
    #print(lastline_arr)
    
    print("l: ")
    print(len(lastline_arr))
    lastline=lastline_arr[len(lastline_arr)-1]
    print("lastline: "+lastline)
    print("lastline-2: "+lastline_arr[len(lastline_arr)-2])
    cidlastline=getIDofLine(lastline)
    aidkey="-1"
    if cidlastline != "-1":
        i=len(lastline_arr)-2
        #search for nex aid entry
        while i >= 0 and "AID" not in lastline_arr[i]:
            i-=1
        if i >= 0:
            aid=getIDofLine(lastline_arr[i])
            if aid != "-1":
                aidkey=aid
    #remove the last line and put the array back together
    
    lastline_arr_list=list(lastline_arr)
    #lastline_arr_list.remove(lastline)
    xml2="\n".join(lastline_arr_list)
    tempfile.write(xml2)
    #add the last tags
    #tempfile.write("</Information></InformationList>")
    tempfile.close()
    parser.parse(open("tempfile","r"))
    dic=handler.ergebnis
    
    #add the last line
    #if cidlastline != "-1":
    #    dic[aidkey].append(cidlastline)
    return dic


def main(args):
    aid_cid_dict=getAllCidsForAssayActivity(args.target)
    write_to_csv(aid_cid_dict, args.outfile)
    
if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument('--outfile', type=argparse.FileType('w'),
        help="Specify output file")
    parser.add_argument('--target', type=str,
        help="Specify output file")
    if len(sys.argv) < 2:
        print "Too few arguments..."
        parser.print_help()
        exit(1)
    args = parser.parse_args()
    main( args )