view rest_tool_assay_by_activity_or_target.py @ 6:9ee84d9fd3a7 draft

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#!/usr/bin/env python

import sys, os
import argparse
import readfile

def main(args):
    #search for acitivity or target
    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/"
    if args.activity is None:
        #target
        url+="target/"+args.targettype+"/"+args.targetid
    else:
        url+="activity/"+args.activity
    url+="/aids/txt"
    data=readfile.getresult(url)
    args.outfile.write(data)
    args.outfile.close()
    
    
if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument('--activity', type=str,
        help="Activities you are looking for")
    parser.add_argument('--target-type', dest="target_type", type=str,
        help="The target identifier type")
    parser.add_argument('--target-id', dest="target_id", type=str,
        help="The specific target")
    parser.add_argument('--outfile', type=argparse.FileType('w'), required=True,
        help="Specify output file")
    if len(sys.argv) < 2:
        print "Too few arguments..."
        parser.print_help()
        exit(1)
    args = parser.parse_args()
    main( args )