bioruby(1)
NAME
br_bioflat.rb -- OBDA flat file indexer
SYNOPSIS
Search:
br_bioflat.rb [--search] [options...]
br_bioflat.rb [--search] [--location DIR] [--dbname DBNAME] [options...] [KEYWORDS]
Create index:
br_bioflat.rb [--create] [--location DIR] [--dbname DBNAME] [--format genbank|embl|fasta] [options...] [--files FILES...]
Update index:
br_bioflat.rb [--update] [--location DIR] [--dbname DBNAME] [options...] [--files FILES...]
Show namespaces:
br_bioflat.rb [--show-namespaces] [--location DIR] [--dbname DBNAME]
[DIR/DBNAME]
br_bioflat.rb [--show-namespaces] [--format=CLASS]
br_bioflat.rb [--show-namespaces] [--files file]
DESCRIPTION
This manual page documents briefly the br_bioflat.rb.
br_bioflat.rb is an OBDA flat file indexer.
OPTIONS
--search Search a database for keywords.
- --namespace --name
- Only valid with the --search option. Set the search namespace. You can set this option multiple times to specify more than one namespace.
- --create Create an index.
- --location
- Specify the directory.
- --dbname Specify the name of the database.
- --primary --secondary
- Set the primary and secondarynamespace of the index. Default primary/secondary namespaces depend on the format of the flatfiles. Only valid with the --create option.
- --add-secondary
- Add secondary namespaces to the default specification. You can use this option many times. Only valid with the --create option.
- --update Update an index
- --sort Sort an index. You can set this to a path to an external
- sorting program, or BUILTIN to use the builtin sort module. This option is only valid with --create (or --update) and --type flat options.
- --renew Re-read all flatfiles and update whole index. This option is
- only valid with the --update option.
- --show-namespaces
- Display the namespaces for an index file.
AUTHOR
This manual page was written by David Nusinow dnusinow@debian.org for
the Debian system (but may be used by others). Permission is granted
to copy, distribute and/or modify this document under the terms of the
GNU General Public License, Version 2 any later version published by
the Free Software Foundation.
- On Debian systems, the complete text of the GNU General Public License
can be found in /usr/share/common-licenses/GPL.