GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
Bio::DB::SeqFeature::Store::DBI::SQLite(3) User Contributed Perl Documentation Bio::DB::SeqFeature::Store::DBI::SQLite(3)
 

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
  $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);

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.

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 - Nathan.Weeks@ars.usda.gov
Copyright (c) 2009 Nathan Weeks
Modified 2010 to support cumulative statistics by Lincoln Stein <lincoln.stein@gmail.com>.
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.
2019-01-01 perl v5.28.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.