---
name: "br_bioflat"
section: "1"
platform: "linux"
package: "ruby-bio"
version: "1.5.2-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/br_bioflat"
---

# br\_bioflat(1)

OBDA flat file indexer

## 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.