Mercurial > repos > iuc > ncbi_eutils_egquery

comparison elink.py @ 0:22fed2340d2b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
author iuc
date Sat, 31 Oct 2015 12:45:31 -0400
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children 3ebc86b520d7
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-1:000000000000 0:22fed2340d2b
1 #!/usr/bin/env python
2 import argparse
3 import eutils
4 import json
5
6
7 if __name__ == '__main__':
8 parser = argparse.ArgumentParser(description='EFetch', epilog='')
9 parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)')
10 parser.add_argument('dbfrom', help='Database containing input UIDs')
11 parser.add_argument('cmd', choices=['neighbor', 'neighbor_score',
12 'neighbor_history', 'acheck', 'ncheck', 'lcheck',
13 'llinks', 'llinkslib', 'prlinks'],
14 help='ELink command mode')
15 # Only used in case of neighbor_history
16 parser.add_argument('--history_out', type=argparse.FileType('w'),
17 help='Output history file', default='-')
18
19 parser.add_argument('--user_email', help="User email")
20 parser.add_argument('--admin_email', help="Admin email")
21 # ID Sources
22 parser.add_argument('--id_list', help='list of ids')
23 parser.add_argument('--id', help='Comma separated individual IDs')
24 parser.add_argument('--history_file', help='Fetch results from previous query')
25
26 # TODO: dates, linkname, term, holding
27 # neighbor or neighbor_history and dbfrom is pubmed
28 # parser.add_argument('--datetype', help='Date type')
29 # parser.add_argument('--reldate', help='In past N days')
30 # parser.add_argument('--mindate', help='Minimum date')
31 # parser.add_argument('--maxdate', help='maximum date')
32
33 # Output
34 args = parser.parse_args()
35
36 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
37 merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
38
39 payload = {
40 'dbfrom': args.dbfrom,
41 'cmd': args.cmd,
42 }
43 if args.history_file is not None:
44 payload.update(c.get_history())
45 else:
46 payload['id'] = ','.join(merged_ids)
47
48 # DB can be 'none' in a few cases.
49 if args.db != "none":
50 payload['db'] = args.db
51
52 results = c.link(**payload)
53
54 if args.cmd == "neighbor_history":
55 history = c.extract_history(results)
56 args.history_out.write(json.dumps(history, indent=4))
57
58 print results