NAME

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

SYNOPSIS

  $cachedb = Bio::DB::FileCache->new($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.

CONTACT

Lincoln Stein <lstein@cshl.org>

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:

  http://bugzilla.open-bio.org/

APPENDIX

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq