Mercurial > repos > iuc > ncbi_eutils_efetch
view elink.py @ 1:0fc65a60436f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author | iuc |
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date | Tue, 30 Oct 2018 19:08:30 -0400 |
parents | 71bcf87a7031 |
children | c09fcbe4b16a |
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#!/usr/bin/env python from __future__ import print_function 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)