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)

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

NAME

       dbsplit - script to split an input set of database(s) into smaller pieces

SYNOPSIS

	 dbsplit.PLS --size 50 [-i inputfile] [-if inputformat] [-of outputformat]
		     [--prefix outputprefix] [ < file1 file 2  OR file1 file2]

DESCRIPTION

       This script will take as input a list of filenames or a single file or from STDIN a sequence database and split the database into separate
       files of X numbers of sequences.  You specify X with the "--size/-s" parameter.	The input and output sequence format is any that is
       supported by bioperl (fasta,embl,genbank,gcg, swissprot, etc).

       You can specify the input data either as a single file with -i filename, or as a single file as an argument like

	 % dbsplit file1 file2

       or as a list of sequence data with

	 % cat file1 file2 file3 | dbsplit

       You'll want to use the "--prefix" to specify what the output prefix will be.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Jason Stajich, jason-at-bioperl-dot-org

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