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br_bioflat.rb — OBDA flat file indexer

BIORUBY(1) General Commands Manual 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.
 
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