Mercurial > repos > iuc > ncbi_eutils_einfo
diff elink.py @ 0:32ac58827a97 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author | iuc |
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date | Thu, 07 Jul 2016 02:40:06 -0400 |
parents | |
children | 5b1dc5936af2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/elink.py Thu Jul 07 02:40:06 2016 -0400 @@ -0,0 +1,59 @@ +#!/usr/bin/env python +import argparse +import json + +import eutils + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='EFetch', epilog='') + parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)') + parser.add_argument('dbfrom', help='Database containing input UIDs') + parser.add_argument('cmd', choices=['neighbor', 'neighbor_score', + 'neighbor_history', 'acheck', 'ncheck', 'lcheck', + 'llinks', 'llinkslib', 'prlinks'], + help='ELink command mode') + # Only used in case of neighbor_history + parser.add_argument('--history_out', type=argparse.FileType('w'), + help='Output history file', default='-') + + parser.add_argument('--user_email', help="User email") + parser.add_argument('--admin_email', help="Admin email") + # ID Sources + 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') + + # TODO: dates, linkname, term, holding + # neighbor or neighbor_history and dbfrom is pubmed + # parser.add_argument('--datetype', help='Date type') + # parser.add_argument('--reldate', help='In past N days') + # parser.add_argument('--mindate', help='Minimum date') + # parser.add_argument('--maxdate', help='maximum date') + + # Output + 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 = { + 'dbfrom': args.dbfrom, + 'cmd': args.cmd, + } + if args.history_file is not None: + payload.update(c.get_history()) + else: + payload['id'] = ','.join(merged_ids) + + # DB can be 'none' in a few cases. + if args.db != "none": + payload['db'] = args.db + + results = c.link(**payload) + + if args.cmd == "neighbor_history": + history = c.extract_history(results) + args.history_out.write(json.dumps(history, indent=4)) + + print results