Bio::DB::FileCache - In file cache for BioSeq objects

       The rest of the documentation details each of the object methods. Internal methods are usually preceded
       with a _

   new
        Title   : new
        Usage   : $db = Bio::DB::FileCache->new(
                        -seqdb => $db,   # Bio::DB::RandomAccessI database
                        -file  => $path, # path to index file
                        -keep  => $flag, # don't unlink index file
                 )
        Function: creates a new on-disk cache
        Returns : a Bio::DB::RandomAccessI database
        Args    : as above
        Throws  : "Must be a randomaccess database" exception
                  "Could not open primary index file" exception

       If no index file is specified, will create a temporary file in your system's temporary file directory.
       The name of this temporary file can be retrieved using file_name().

   get_Seq_by_id
        Title   : get_Seq_by_id
        Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
        Function: Gets a Bio::Seq object by its name
        Returns : a Bio::Seq object
        Args    : the id (as a string) of a sequence
        Throws  : "id does not exist" exception

   get_Seq_by_acc
        Title   : get_Seq_by_acc
        Usage   : $seq = $db->get_Seq_by_acc('X77802');
        Function: Gets a Bio::Seq object by accession number
        Returns : A Bio::Seq object
        Args    : accession number (as a string)
        Throws  : "acc does not exist" exception

   seqdb
        Title   : seqdb
        Usage   : $seqdb = $db->seqdb([$seqdb])
        Function: gets/sets the Bio::DB::RandomAccessI database
        Returns : a Bio::DB::RandomAccessI database
        Args    : new sequence database (optional)
        Throws  : nothing

   file_name
        Title   : file_name
        Usage   : $path = $db->file_name([$file_name])
        Function: gets/sets the name of the cache file
        Returns : a path
        Args    : new cache file name (optional)
        Throws  : nothing

       It probably isn't useful to set the cache file name after you've opened it.

   keep
        Title   : keep
        Usage   : $keep = $db->keep([$flag])
        Function: gets/sets the value of the "keep" flag
        Returns : current value
        Args    : new value (optional)
        Throws  : nothing

       The keep flag will cause the index file to be unlinked when the process exits.  Since on some operating
       systems (Unix, OS/2) the unlinking occurs during the new() call immediately after opening the file, it
       probably isn't safe to change this value.

   db
        Title   : db
        Usage   : $db->db
        Function: returns tied hash to index database
        Returns : a Berkeley DB tied hashref
        Args    : none
        Throws  : nothing

   flush
        Title   : flush
        Usage   : $db->flush
        Function: flushes the cache
        Returns : nothing
        Args    : none
        Throws  : nothing

   get_Seq_by_version
        Title   : get_Seq_by_version
        Usage   : $seq = $db->get_Seq_by_version('X77802.1');
        Function: Gets a Bio::Seq object by sequence version
        Returns : A Bio::Seq object
        Args    : accession.version (as a string)
        Throws  : "acc.version does not exist" exception

perl v5.32.1                                       2021-08-15                            Bio::DB::FileCache(3pm)

       Lincoln Stein <lstein@cshl.org>

   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.

   ReportingBugs
       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

       Bio::DB::FileCache - In file cache for BioSeq objects

         $cachedb = Bio::DB::FileCache->new($real_db);

         #
         # $real_db is a Bio::DB::RandomAccessI database
         #

         $seq = $cachedb->get_Seq_by_id('ROA1_HUMAN');

         #
         # $seq is a Bio::Seq object
         #

         # more control provided with named-parameter form

         $cachedb = Bio::DB::FileCache->new( -seqdb => $real_db,
                                             -file  => $path,
                                             -keep  => $flag,
                                           );
       =head1 DESCRIPTION

       This is a disk cache system which saves the objects returned by Bio::DB::RandomAccessI on disk.  The disk
       cache grows without limit, while the process is running, but is automatically unlinked at process
       termination unless the -keep flag is set.

       This module requires DB_File and Storable.