Mercurial > repos > iuc > ncbi_eutils_efetch
view efetch.py @ 2:0977ec0f3ba8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
author | iuc |
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date | Wed, 11 Mar 2020 04:03:36 -0400 |
parents | 0fc65a60436f |
children | c09fcbe4b16a |
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#!/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') 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, ftype=args.retmode, **payload)