Bio::DB::GFF::Adaptor:UserkContributed PerBio::DB::GFF::Adaptor::berkeleydb(3)NAMEBio::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 v5.14.12011-07-Bio::DB::GFF::Adaptor::berkeleydb(3)