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]


This manual page documents briefly the br_bioflat.rb.

br_bioflat.rb is an OBDA flat file indexer.



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 an index.


Specify the directory.


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 namespaces to the default specification. You can use this option many times. Only valid with the --create option.


Update an index


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.


Re-read all flatfiles and update whole index. This option is only valid with the --update option.


Display the namespaces for an index file.


This manual page was written by David Nusinow [email protected] 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.