br_bioflat - Online in the Cloud

PROGRAM:

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.

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