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Bio::DB::SeqFeature::SUser:ContributBio::DB::SeqFeature::Store::DBI::SQLite(3)

NAME
       Bio::DB::SeqFeature::Store::DBI::SQLite -- 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.

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

AUTHOR
       Nathan Weeks - Nathan.Weeks@ars.usda.gov

       Copyright (c) 2009 Nathan Weeks

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

perl v5.14.1			  20Bio::DB::SeqFeature::Store::DBI::SQLite(3)
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