Mercurial > repos > iuc > ncbi_eutils_efetch

comparison efetch.py @ 0:71bcf87a7031 draft

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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 02:39:36 -0400
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children 0fc65a60436f
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-1:000000000000 0:71bcf87a7031
1 #!/usr/bin/env python
2 import argparse
3 import eutils
4
5
6 if __name__ == '__main__':
7 parser = argparse.ArgumentParser(description='EFetch', epilog='')
8 parser.add_argument('db', help='Database to use')
9 parser.add_argument('--user_email', help="User email")
10 parser.add_argument('--admin_email', help="Admin email")
11
12 # ID source
13 parser.add_argument('--id_list', help='list of ids')
14 parser.add_argument('--id', help='Comma separated individual IDs')
15 parser.add_argument('--history_file', help='Fetch results from previous query')
16
17 # Output
18 parser.add_argument('--retmode', help='Retmode')
19 parser.add_argument('--rettype', help='Rettype')
20 args = parser.parse_args()
21
22 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
23 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
24
25 payload = {}
26 if args.history_file is not None:
27 payload.update(c.get_history())
28 else:
29 payload['id'] = ','.join(merged_ids)
30
31 for attr in ('retmode', 'rettype'):
32 if getattr(args, attr, None) is not None:
33 payload[attr] = getattr(args, attr)
34
35 c.fetch(args.db, ftype=args.retmode, **payload)