Provided by: libbio-perl-perl_1.7.2-2_all bug


       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);
         $seq       = $db->get_Seq_by_id('HSFOS');
         @sequences = $db->get_Seq_by_acc('DIV' => 'primate');
         $raw       = $db->fetch_raw('HSFOS');


       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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AUTHOR - Lincoln Stein

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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.

   To Be Implemented in Subclasses
       The following methods MUST be implemented by subclasses.

   May Be Overridden in Subclasses
       The following methods MAY be overridden by subclasses.