Mercurial > repos > iuc > ncbi_eutils_egquery

comparison efetch.py @ 5:20a86bfb54eb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author iuc
date Thu, 07 Jul 2016 02:38:00 -0400
parents 22fed2340d2b
children 2d54a753d1f1
comparison
equal deleted inserted replaced
4:484b84b30c75 5:20a86bfb54eb
15 parser.add_argument('--history_file', help='Fetch results from previous query') 15 parser.add_argument('--history_file', help='Fetch results from previous query')
16 16
17 # Output 17 # Output
18 parser.add_argument('--retmode', help='Retmode') 18 parser.add_argument('--retmode', help='Retmode')
19 parser.add_argument('--rettype', help='Rettype') 19 parser.add_argument('--rettype', help='Rettype')
20 parser.add_argument('--whole', action='store_true',
21 help='Download all records associated with query')
22 args = parser.parse_args() 20 args = parser.parse_args()
23 21
24 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) 22 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
25 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file) 23 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
26 24
32 30
33 for attr in ('retmode', 'rettype'): 31 for attr in ('retmode', 'rettype'):
34 if getattr(args, attr, None) is not None: 32 if getattr(args, attr, None) is not None:
35 payload[attr] = getattr(args, attr) 33 payload[attr] = getattr(args, attr)
36 34
37 c.fetch(args.db, whole=args.whole, **payload) 35 c.fetch(args.db, ftype=args.retmode, **payload)