Christopher Fields > BioPerl > Bio::DB::SeqFeature::Store::DBI::SQLite



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Bio::DB::SeqFeature::Store::DBI::SQLite -- SQLite implementation of Bio::DB::SeqFeature::Store


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

  # Open the sequence database
  my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::SQLite',
                                           -dsn     => '/path/to/database.db');

  # 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
  $db->update($f) or die "Couldn't update!";

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

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

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

  # type
  @features = $db->get_features_by_name('gene');

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

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

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

  # 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']);

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

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

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


Bio::DB::SeqFeature::Store::SQLite is the SQLite 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 SQLite adaptor

To establish a connection to the database, call Bio::DB::SeqFeature::Store->new(-adaptor=>'DBI::SQLite',@more_args). The additional arguments are as follows:

  Argument name       Description
  -------------       -----------

 -dsn              The path to the SQLite database file.

 -namespace        A prefix to attach to each table. This allows you
                   to have several virtual databases in the same
                   physical database.

 -temp             Boolean flag. If true, a temporary database
                   will be created and destroyed as soon as
                   the Store object goes out of scope. (synonym -temporary)

 -autoindex        Boolean flag. If true, features in the database will be
                   reindexed every time they change. This is the default.

 -fts              Boolean flag. If true, when the -create flag is true, the
                   attribute table will be created and indexed index for
                   full-text search using the most recent FTS extension
                   supported by DBD::SQLite.

 -tmpdir           Directory in which to place temporary files during "fast" loading.
                   Defaults to File::Spec->tmpdir(). (synonyms -dump_dir, -dumpdir, -tmp)

 -dbi_options      A hashref to pass to DBI->connect's 4th argument, the "attributes."
                   (synonyms -options, -dbi_attr)

 -write            Pass true to open database for writing or updating.

If successful, a new instance of Bio::DB::SeqFeature::Store::DBI::SQLite will be returned.

In addition to the standard methods supported by all well-behaved Bio::DB::SeqFeature::Store databases, several following adaptor-specific methods are provided. These are described in the next sections.


 Title   : toplevel_types
 Usage   : @type_list = $db->toplevel_types
 Function: Get the toplevel types in the database
 Returns : array of Bio::DB::GFF::Typename objects
 Args    : none
 Status  : public

This is similar to types() but only returns the types of INDEXED (toplevel) features.


Nathan Weeks -

Copyright (c) 2009 Nathan Weeks

Modified 2010 to support cumulative statistics by Lincoln Stein <>.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See the Bioperl license for more details.

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