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Bio::DB::GFF::Adaptor:UserkContributed PerBio::DB::GFF::Adaptor::berkeleydb(3)

NAME
       Bio::DB::GFF::Adaptor::berkeleydb -- Bio::DB::GFF database adaptor for
       in-memory databases

SYNOPSIS
	 use Bio::DB::GFF;
	 my $db = Bio::DB::GFF->new(-adaptor=> 'berkeleydb',
				    -create => 1, # on initial build you need this
				    -dsn    => '/usr/local/share/gff/dmel');

	 # initialize an empty database, then load GFF and FASTA files
	 $db->initialize(1);
	 $db->load_gff('/home/drosophila_R3.2.gff');
	 $db->load_fasta('/home/drosophila_R3.2.fa');

	 # do queries
	 my $segment  = $db->segment(Chromosome => '1R');
	 my $subseg   = $segment->subseq(5000,6000);
	 my @features = $subseg->features('gene');

       See Bio::DB::GFF for other methods.

DESCRIPTION
       This adaptor implements a berkeleydb-indexed version of Bio::DB::GFF.
       It requires the DB_File and Storable modules. It can be used to store
       and retrieve short to medium-length GFF files of several million
       features in length.

CONSTRUCTOR
       Use Bio::DB::GFF->new() to construct new instances of this class.
       Three named arguments are recommended:

	Argument    Description
	--------    -----------

	-adaptor    Set to "berkeleydb" to create an instance of this class.

	-dsn	    Path to directory where the database index files will be stored (alias -db)

	-autoindex  Monitor the indicated directory path for FASTA and GFF files, and update the
		      indexes automatically if they change (alias -dir)

	-write	    Set to a true value in order to update the database.

	-create	    Set to a true value to create the database the first time
		      (implies -write)

	-tmp	    Location of temporary directory for storing intermediate files
		      during certain queries.

	-preferred_groups  Specify the grouping tag. See L<Bio::DB::GFF>

       The -dsn argument selects the directory in which to store the database
       index files. If the directory does not exist it will be created
       automatically, provided that the current process has sufficient
       privileges. If no -dsn argument is specified, a database named "test"
       will be created in your system's temporary files directory.

       The -tmp argument specifies the temporary directory to use for storing
       intermediate search results. If not specified, your system's temporary
       files directory will be used. On Unix systems, the TMPDIR environment
       variable is honored. Note that some queries can require a lot of space.

       The -autoindex argument, if present, selects a directory to be
       monitored for GFF and FASTA files (which can be compressed with the
       gzip program if desired). Whenever any file in this directory is
       changed, the index files will be updated. Note that the indexing can
       take a long time to run: anywhere from 5 to 10 minutes for a million
       features. An alias for this argument is -dir, which gives this adaptor
       a similar flavor to the "memory" adaptor.

       -dsn and -dir can point to the same directory. If -dir is given but
       -dsn is absent the index files will be stored into the directory
       containing the source files.  For autoindexing to work, you must
       specify the same -dir path each time you open the database.

       If you do not choose autoindexing, then you will want to load the
       database using the bp_load_gff.pl command-line tool. For example:

	bp_load_gff.pl -a berkeleydb -c -d /usr/local/share/gff/dmel dna1.fa dna2.fa features.gff

METHODS
       See Bio::DB::GFF for inherited methods

BUGS
       The various get_Stream_* methods and the features() method with the
       -iterator argument only return an iterator after the query runs
       completely and the module has been able to generate a temporary results
       file on disk. This means that iteration is not as big a win as it is
       for the relational-database adaptors.

       Like the dbi::mysqlopt adaptor, this module uses a binning scheme to
       speed up range-based searches. The binning scheme used here imposes a
       hard-coded 1 gigabase (1000 Mbase) limit on the size of the largest
       chromosome or other reference sequence.

SEE ALSO
       Bio::DB::GFF, bioperl

AUTHORS
       Vsevolod (Simon) Ilyushchenko >simonf@cshl.edu< Lincoln Stein
       >lstein@cshl.edu<

       Copyright (c) 2005 Cold Spring Harbor Laboratory.

       This library is free software; you can redistribute it and/or modify it
       under the same terms as Perl itself.

   _feature_by_name
	Title	: _feature_by_name
	Usage	: $db->get_features_by_name($class,$name,$callback)
	Function: get a list of features by name and class
	Returns : count of number of features retrieved
	Args	: name of feature, class of feature, and a callback
	Status	: protected

       This method is used internally.	The callback arguments are those used
       by make_feature().

perl v5.14.1			  2011-07-Bio::DB::GFF::Adaptor::berkeleydb(3)
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