/ 
BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ 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>

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.

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:

https://github.com/bioperl/bioperl-live/issues

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