Bio::DB::Flat - Interface for indexed flat files
$db = Bio::DB::Flat->new(-directory => '/usr/share/embl', -dbname => 'mydb', -format => 'embl', -index => 'bdb', -write_flag => 1); $db->build_index('/usr/share/embl/primate.embl', '/usr/share/embl/protists.embl'); $seq = $db->get_Seq_by_id('BUM'); @sequences = $db->get_Seq_by_acc('DIV' => 'primate'); $raw = $db->fetch_raw('BUM');
This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see Bio::Index::Abstract), this is specialized to work with the "flat index" and BerkeleyDB indexed flat file formats worked out at the 2002 BioHackathon.
This object is a general front end to the underlying databases.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore).
Title : new Usage : my $db = Bio::DB::Flat->new( -directory => $root_directory, -dbname => 'mydb', -write_flag => 1, -index => 'bdb', -verbose => 0, -out => 'outputfile', -format => 'genbank'); Function: create a new Bio::DB::Flat object Returns : new Bio::DB::Flat object Args : -directory Root directory containing "config.dat" -write_flag If true, allows creation/updating. -verbose Verbose messages -out File to write to when write_seq invoked -index 'bdb' or 'binarysearch' Status : Public
The required -directory argument indicates where the flat file indexes will be stored. The build_index() and write_seq() methods will automatically create subdirectories of this root directory. Each subdirectory will contain a human-readable configuration file named "config.dat" that specifies where the individual indexes are stored.
The required -dbname argument gives a name to the database index. The index files will actually be stored in a like-named subdirectory underneath the root directory.
The -write_flag enables writing new entries into the database as well as the creation of the indexes. By default the indexes will be opened read only.
-index is one of "bdb" or "binarysearch" and indicates the type of index to generate. "bdb" corresponds to Berkeley DB. You *must* be using BerkeleyDB version 2 or higher, and have the Perl BerkeleyDB extension installed (DB_File will *not* work). "binarysearch" corresponds to the OBDA "flat" indexed file.
The -out argument specifies the output file for writing objects created with write_seq().
The -format argument specifies the format of the input file or files. If the file suffix is one that Bioperl can already associate with a format then this is optional.
Title : new_from_registry Usage : $db = Bio::DB::Flat->new_from_registry(%config) Function: creates a new Bio::DB::Flat object in a Bio::DB::Registry- compatible fashion Returns : new Bio::DB::Flat Args : provided by the registry, see below Status : Public
The following registry-configuration tags are recognized:
location Root of the indexed flat file; corresponds to the new() method's -directory argument.
Title : fetch Usage : $index->fetch( $id ) Function: Returns a Bio::Seq object from the index Example : $seq = $index->fetch( 'dJ67B12' ) Returns : Bio::Seq object Args : ID
Deprecated. Use get_Seq_by_id instead.
The following methods MUST be implemented by subclasses.
The following methods MAY be overridden by subclasses.