$cachedb = Bio::DB::FileCache->new($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,
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.
CONTACTLincoln Stein <[email protected]>
SupportPlease direct usage questions or support issues to the mailing list:
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 BugsReport 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:
APPENDIXThe 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