Mercurial > repos > iuc > ncbi_eutils_egquery
diff efetch.py @ 0:22fed2340d2b draft
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 |
| parents | |
| children | 20a86bfb54eb |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/efetch.py Sat Oct 31 12:45:31 2015 -0400 @@ -0,0 +1,37 @@ +#!/usr/bin/env python +import argparse +import eutils + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='EFetch', epilog='') + parser.add_argument('db', help='Database to use') + parser.add_argument('--user_email', help="User email") + parser.add_argument('--admin_email', help="Admin email") + + # ID source + parser.add_argument('--id_list', help='list of ids') + parser.add_argument('--id', help='Comma separated individual IDs') + parser.add_argument('--history_file', help='Fetch results from previous query') + + # Output + parser.add_argument('--retmode', help='Retmode') + parser.add_argument('--rettype', help='Rettype') + parser.add_argument('--whole', action='store_true', + help='Download all records associated with query') + args = parser.parse_args() + + c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) + merged_ids = c.parse_ids(args.id_list, args.id, args.history_file) + + payload = {} + if args.history_file is not None: + payload.update(c.get_history()) + else: + payload['id'] = ','.join(merged_ids) + + for attr in ('retmode', 'rettype'): + if getattr(args, attr, None) is not None: + payload[attr] = getattr(args, attr) + + c.fetch(args.db, whole=args.whole, **payload)
