bp_bioflat_index(1p) [debian man page]

BP_BIOFLAT_INDEX(1p)					User Contributed Perl Documentation				      BP_BIOFLAT_INDEX(1p)

NAME

       bioflat_index.pl - index sequence files using Bio::DB::Flat

DESCRIPTION

	Create or update a biological sequence database indexed with the
	Bio::DB::Flat indexing scheme.	The arguments are a list of flat files
	containing the sequence information to be indexed.

USAGE

	bioflat_index.pl <options> file1 file2 file3...

	Options:

	    --create		  Create or reinitialize the index.  If not specified,
				  the index must already exist.

	    --format   <format>   The format of the sequence files.  Must be one
				  of "genbank", "swissprot", "embl" or "fasta".

	    --location <path>	  Path to the directory in which the index files
				  are stored.

	    --dbname <name>	  The symbolic name of the database to be created.

	    --indextype <type>	  Type of index to create.  Either "bdb" or "flat".
				  "binarysearch" is the same as "flat".

       Options can be abbreviated.  For example, use -i for --indextype.

       The following environment variables will be used as defaults if the corresponding options are not provided:

	    OBDA_FORMAT      format of sequence file
	    OBDA_LOCATION    path to directory in which index files are stored
	    OBDA_DBNAME      name of database
	    OBDA_INDEX	     type of index to create

perl v5.14.2							    2012-03-02						      BP_BIOFLAT_INDEX(1p)

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.

																	BIORUBY(1)