Bio::DB::SeqFeature::Store::berkeleydb(3)

NAME
Bio::DB::SeqFeature::Store::berkeleydb -- Storage and retrieval of sequence annotation data in Berkeleydb files

SYNOPSIS
  use Bio::DB::SeqFeature::Store;

  # Create a database from the feature files located in /home/fly4.3 and store
  # the database index in the same directory:
  my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                            -dir     => '/home/fly4.3');

  # Create a database that will monitor the files in /home/fly4.3, but store
  # the indexes in /var/databases/fly4.3
  $db    = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                            -dir     => '/home/fly4.3',
                                            -dsn     => '/var/databases/fly4.3');

  # Create a feature database from scratch
  $db    = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                            -dsn     => '/var/databases/fly4.3',
                                            -create  => 1);

  # get a feature from somewhere
  my $feature = Bio::SeqFeature::Generic->new(...);

  # store it
  $db->store($feature) or die "Couldn't store!";

  # primary ID of the feature is changed to indicate its primary ID
  # in the database...
  my $id = $feature->primary_id;

  # get the feature back out
  my $f  = $db->fetch($id);

  # change the feature and update it
  $f->start(100);
  $db->update($f) or $self->throw("Couldn't update!");

  # use the GFF3 loader to do a bulk write:
  my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store   => $db,
                                                           -verbose => 0,
                                                           -fast    => 1);
  $loader->load('/home/fly4.3/dmel-all.gff');

  # searching...
  # ...by id
  my @features = $db->fetch_many(@list_of_ids);

  # ...by name
  @features = $db->get_features_by_name('ZK909');

  # ...by alias
  @features = $db->get_features_by_alias('sma-3');

  # ...by type
  @features = $db->get_features_by_type('gene');

  # ...by location
  @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000);

  # ...by attribute
  @features = $db->get_features_by_attribute({description => 'protein kinase'})

  # ...by the GFF "Note" field
  @result_list = $db->search_notes('kinase');

  # ...by arbitrary combinations of selectors
  @features = $db->features(-name => $name,
                            -type => $types,
                            -seq_id => $seqid,
                            -start  => $start,
                            -end    => $end,
                            -attributes => $attributes);

  # ...using an iterator
  my $iterator = $db->get_seq_stream(-name => $name,
                                     -type => $types,
                                     -seq_id => $seqid,
                                     -start  => $start,
                                     -end    => $end,
                                     -attributes => $attributes);

  while (my $feature = $iterator->next_seq) {
    # do something with the feature
  }

  # ...limiting the search to a particular region
  my $segment  = $db->segment('Chr1',5000=>6000);
  my @features = $segment->features(-type=>['mRNA','match']);

  # what feature types are defined in the database?
  my @types    = $db->types;

  # getting & storing sequence information
  # Warning: this returns a string, and not a PrimarySeq object
  $db->insert_sequence('Chr1','GATCCCCCGGGATTCCAAAA...');
  my $sequence = $db->fetch_sequence('Chr1',5000=>6000);

  # create a new feature in the database
  my $feature = $db->new_feature(-primary_tag => 'mRNA',
                                 -seq_id      => 'chr3',
                                 -start      => 10000,
                                 -end        => 11000);

DESCRIPTION
Bio::DB::SeqFeature::Store::berkeleydb is the Berkeleydb adaptor for Bio::DB::SeqFeature::Store. You will not create it directly, but instead use Bio::DB::SeqFeature::Store->new() to do so.

See Bio::DB::SeqFeature::Store for complete usage instructions.

  Using the berkeleydb adaptor
The Berkeley database consists of a series of Berkeleydb index files, and a couple of special purpose indexes. You can create the index files from scratch by creating a new database and calling new_feature() repeatedly, you can create the database and then bulk populate it using the GFF3 loader, or you can monitor a directory of preexisting GFF3 and FASTA files and rebuild the indexes whenever one or more of the fields changes. The last mode is probably the most convenient. Note that the indexer will only pay attention to files that end with .gff3, .wig and .fa.

The new() constructor
    The new() constructor method all the arguments recognized by Bio::DB::SeqFeature::Store, and a few additional ones.

    Standard arguments:

     Name               Value
     ----               -----

     -adaptor           The name of the Adaptor class (default DBI::mysql)

     -serializer        The name of the serializer class (default Storable)

     -index_subfeatures Whether or not to make subfeatures searchable
                        (default true)

     -cache             Activate LRU caching feature -- size of cache

     -compress          Compresses features before storing them in database
                        using Compress::Zlib

    Adaptor-specific arguments

     Name               Value
     ----               -----

     -dsn               Where the index files are stored

     -dir               Where the source (GFF3, FASTA) files are stored

     -autoindex         An alias for -dir.

     -write             Pass true to open the index files for writing.

     -create            Pass true to create the index files if they don't exist
                        (implies -write=>1)

     -locking           Use advisory locking to avoid one process trying to read
                        from the database while another is updating it (may not
                        work properly over NFS).

     -temp              Pass true to create temporary index files that will
                        be deleted once the script exits.

     -verbose           Pass true to report autoindexing operations on STDERR.
                        (default is true).

    Examples:

    To create an empty database which will be populated using calls to store() or new_feature(), or which will be bulk-loaded using the GFF3 loader:

      $db     = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                                 -dsn     => '/var/databases/fly4.3',
                                                 -create  => 1);

    To open a preexisting database in read-only mode:

      $db     = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                                 -dsn     => '/var/databases/fly4.3');

    To open a preexisting database in read/write (update) mode:

      $db     = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                                 -dsn     => '/var/databases/fly4.3',
                                                 -write   => 1);

    To monitor a set of GFF3 and FASTA files located in a directory and create/update the database indexes as needed. The indexes will be stored in a new subdirectory named "indexes":

      $db     = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                                 -dir     => '/var/databases/fly4.3');

    As above, but store the source files and index files in separate directories:

      $db     = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                                 -dsn     => '/var/databases/fly4.3',
                                                 -dir     => '/home/gff3_files/fly4.3');

    To be indexed, files must end with one of .gff3 (GFF3 format), .fa (FASTA format) or .wig (WIG format).

    -autoindex is an alias for -dir.

    You should specify -locking in a multiuser environment, including the case in which the database is being used by a web server at the same time another user might be updating it.

See Bio::DB::SeqFeature::Store for all the access methods supported by this adaptor. The various methods for storing and updating features and sequences into the database are supported, but there is no locking. If two processes try to update the same database simultaneously, the database will likely become corrupted.

BUGS
This is an early version, so there are certainly some bugs. Please use the BioPerl bug tracking system to report bugs.

SEE ALSO
bioperl, Bio::DB::SeqFeature, Bio::DB::SeqFeature::Store, Bio::DB::SeqFeature::GFF3Loader, Bio::DB::SeqFeature::Segment, Bio::DB::SeqFeature::Store::memory, Bio::DB::SeqFeature::Store::DBI::mysql,

AUTHOR
Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2006 Cold Spring Harbor Laboratory.

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