Bio::DB::SeqFeature::Store::DBI::SQLite(3) SQLite implementation of Bio::DB::SeqFeature::Store

SYNOPSIS


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
$f->start(100);
$db->update($f) or die "Couldn't update!";
# 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_name('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']);
# 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);
# 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);

DESCRIPTION

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.
 -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.

toplevel_types

 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.

AUTHOR

Nathan Weeks - [email protected]

Copyright (c) 2009 Nathan Weeks

Modified 2010 to support cumulative statistics by Lincoln Stein <[email protected]>.

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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