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.
Lincoln Stein <firstname.lastname@example.org>
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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().
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
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
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
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.
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.
Title : db Usage : $db->db Function: returns tied hash to index database Returns : a Berkeley DB tied hashref Args : none Throws : nothing
Title : flush Usage : $db->flush Function: flushes the cache Returns : nothing Args : none Throws : nothing
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