Mercurial > repos > iuc > ncbi_eutils_esearch

comparison elink.py @ 3:49b8084df3ce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
author iuc
date Fri, 10 Jun 2016 14:49:25 -0400
parents 6ba298236729
children af1858733b81
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2:0ea34f262410 3:49b8084df3ce
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import argparse 2 import argparse
3 import json
4
3 import eutils 5 import eutils
4 import json
5 6
6 7
7 if __name__ == '__main__': 8 if __name__ == '__main__':
8 parser = argparse.ArgumentParser(description='EFetch', epilog='') 9 parser = argparse.ArgumentParser(description='EFetch', epilog='')
9 parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)') 10 parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)')
10 parser.add_argument('dbfrom', help='Database containing input UIDs') 11 parser.add_argument('dbfrom', help='Database containing input UIDs')
11 parser.add_argument('cmd', choices=['neighbor', 'neighbor_score', 12 parser.add_argument('cmd', choices=['neighbor', 'neighbor_score',
12 'neighbor_history', 'acheck', 'ncheck', 'lcheck', 13 'neighbor_history', 'acheck', 'ncheck', 'lcheck',
13 'llinks', 'llinkslib', 'prlinks'], 14 'llinks', 'llinkslib', 'prlinks'],
14 help='ELink command mode') 15 help='ELink command mode')
15 # Only used in case of neighbor_history 16 # Only used in case of neighbor_history
16 parser.add_argument('--history_out', type=argparse.FileType('w'), 17 parser.add_argument('--history_out', type=argparse.FileType('w'),
17 help='Output history file', default='-') 18 help='Output history file', default='-')
18 19