/ 
bioperl-1.5.2_004-RCd
/ Bio::DB::FileCache

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