Mercurial > repos > iuc > ncbi_eutils_elink
diff ecitmatch.py @ 0:59063d2e91c6 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 02:40:20 -0400 |
parents | |
children | 2791c731fc65 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ecitmatch.py Thu Jul 07 02:40:20 2016 -0400 @@ -0,0 +1,60 @@ +#!/usr/bin/env python +import argparse +import eutils + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='ECitMatch', epilog='') + parser.add_argument('--file', type=argparse.FileType('r'), help='Tabular file containing citations to search') + + parser.add_argument('--key', nargs='*', help='Citation Key') + parser.add_argument('--journal_title', nargs='*', help='Journal Title') + parser.add_argument('--year', nargs='*', help='Year') + parser.add_argument('--volume', nargs='*', help='Volume') + parser.add_argument('--first_page', nargs='*', help='First Page') + parser.add_argument('--author_name', nargs='*', help='Author name') + + # Emails + parser.add_argument('--user_email', help="User email") + parser.add_argument('--admin_email', help="Admin email") + args = parser.parse_args() + + c = eutils.Client(user_email=args.user_email, admin_email=args.admin_email) + + citations = [] + if args.file is None: + for key, journal, year, volume, first_page, author_name in \ + zip(args.key, args.journal_title, args.year, args.volume, args.first_page, args.author_name): + citations.append({ + 'key': key, + 'journal': journal, + 'year': year, + 'volume': volume, + 'first_page': first_page, + 'author_name': author_name, + }) + else: + for line in args.file: + line = line.strip() + if not line.startswith('#'): + tmp = line.split('\t') + try: + citations.append({ + 'journal': tmp[0], + 'year': tmp[1], + 'volume': tmp[2], + 'first_page': tmp[3], + 'author_name': tmp[4], + 'key': tmp[5], + }) + except KeyError: + print "Could not parse line: %s" % line + + payload = { + 'db': 'pubmed', + 'bdata': citations + } + + results = c.citmatch(**payload) + # We get data back as pipe separated, so just replace those with tabs + print results.replace('|', '\t')