NAME

       Bio::DB::Flat - Interface for indexed flat files

SYNOPSIS

         $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');

DESCRIPTION

       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.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Lincoln Stein

       Email - lstein@cshl.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with an "_" (underscore).

   new
        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.

   new_from_registry
        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.

   fetch
         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.