ENCODE_get_fields.py

#!/usr/bin/env python
# -*- coding: latin-1 -*-
''' BASIC REPORTER SCRIPT
'''
import requests
import json
import sys
import os.path
import argparse
import encodedcc
from base64 import b64encode

HEADERS = {'content-type': 'application/json'}
DEBUG_ON = False
EPILOG = '''Examples:

To use a different key from the default keypair file:

        %(prog)s --key submit
'''

def get_experiment_list(file,search, connection):
        objList = []
        myConnect = connection
        if search == "NULL":
            f = open(file)
            objList = f.readlines()
            for i in range(0, len(objList)):
               objList[i] = objList[i].strip()
        else:
            set = encodedcc.get_ENCODE(search+'&limit=all&frame=embedded', myConnect)
            for i in range(0, len(set['@graph'])):
                #print set['@graph'][i]['accession'] 
                objList.append(set['@graph'][i]['@id'] )
                #objList.append(set['@graph'][i]['uuid'] )

        return objList 
def get_antibody_approval (antibody, target):
        myConnect = connection
        search = encodedcc.get_ENCODE('search/?searchTerm='+antibody+'&type=antibody_approval', myConnect)
        for approval in search['@graph']:
            if approval['target']['name'] == target:
                return approval['status']
        return "UNKNOWN"  

## I need my attachment thing here

def main():

        parser = argparse.ArgumentParser(
            description=__doc__, epilog=EPILOG,
            formatter_class=argparse.RawDescriptionHelpFormatter,
        )
        parser.add_argument('--infile', '-i', default='obList', help="File containing a list of ENCSRs.")
        parser.add_argument('--search', default='NULL', help="The search parameters.")
        parser.add_argument('--key', default='default', help="The keypair identifier from the keyfile.  Default is --key=default")
        parser.add_argument('--keyfile', default=os.path.expanduser("~/keypairs.json"), help="The keypair file.  Default is --keyfile=%s" %(os.path.expanduser("~/keypairs.json")))
        parser.add_argument('--debug', default=False, action='store_true', help="Print debug messages.  Default is False.")
        parser.add_argument('--field', default='accession', help="The field to report.  Default is accession.")
        args = parser.parse_args()

        DEBUG_ON =args.debug

        myKey = encodedcc.ENC_Key(args.keyfile, args.key)
        myConnect = encodedcc.ENC_Connection(myKey)

        #Get list of objects we are interested in

        objList = get_experiment_list (args.infile, args.search, myConnect)
        for i in range (0, len(objList)):
           
           field = ''     
           if objList[i] != '':
               ob = encodedcc.get_ENCODE(objList[i], myConnect)
               id = ob.get('@id')
               if args.field in ob:
                   field = str(ob[args.field])
           else:
              id = objList[i]
           print ('\t'.join([id,field]))

if __name__ == '__main__':
     main()