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.IX Title "Bio::DB::GFF::Adaptor::berkeleydb 3pm"
.TH Bio::DB::GFF::Adaptor::berkeleydb 3pm "2020-01-13" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::GFF::Adaptor::berkeleydb \-\- Bio::DB::GFF database adaptor for in\-memory databases
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 4
\&  use Bio::DB::GFF;
\&  my $db = Bio::DB::GFF\->new(\-adaptor=> \*(Aqberkeleydb\*(Aq,
\&                             \-create => 1, # on initial build you need this
\&                             \-dsn    => \*(Aq/usr/local/share/gff/dmel\*(Aq);
\&
\&  # initialize an empty database, then load GFF and FASTA files
\&  $db\->initialize(1);
\&  $db\->load_gff(\*(Aq/home/drosophila_R3.2.gff\*(Aq);
\&  $db\->load_fasta(\*(Aq/home/drosophila_R3.2.fa\*(Aq);
\&
\&  # do queries
\&  my $segment  = $db\->segment(Chromosome => \*(Aq1R\*(Aq);
\&  my $subseg   = $segment\->subseq(5000,6000);
\&  my @features = $subseg\->features(\*(Aqgene\*(Aq);
.Ve
.PP
See Bio::DB::GFF for other methods.
.SH "DESCRIPTION"
.IX Header "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 \s-1GFF\s0 files of several million
features in length.
.SH "CONSTRUCTOR"
.IX Header "CONSTRUCTOR"
Use Bio::DB::GFF\->\fBnew()\fR to construct new instances of this class.
Three named arguments are recommended:
.PP
.Vb 2
\& 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>
.Ve
.PP
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 \*(L"test\*(R"
will be created in your system's temporary files directory.
.PP
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 \s-1TMPDIR\s0 environment
variable is honored. Note that some queries can require a lot of
space.
.PP
The \-autoindex argument, if present, selects a directory to be
monitored for \s-1GFF\s0 and \s-1FASTA\s0 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 \*(L"memory\*(R" adaptor.
.PP
\&\-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.
.PP
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:
.PP
.Vb 1
\& bp_load_gff.pl \-a berkeleydb \-c \-d /usr/local/share/gff/dmel dna1.fa dna2.fa features.gff
.Ve
.SH "METHODS"
.IX Header "METHODS"
See Bio::DB::GFF for inherited methods
.SH "BUGS"
.IX Header "BUGS"
The various get_Stream_* methods and the \fBfeatures()\fR 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.
.PP
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.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::GFF, bioperl
.SH "AUTHORS"
.IX Header "AUTHORS"
Vsevolod (Simon) Ilyushchenko >simonf@cshl.edu<
Lincoln Stein >lstein@cshl.edu<
.PP
Copyright (c) 2005 Cold Spring Harbor Laboratory.
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
.SS "_feature_by_name"
.IX Subsection "_feature_by_name"
.Vb 6
\& 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
.Ve
.PP
This method is used internally.  The callback arguments are those used
by \fBmake_feature()\fR.