Bio::DB::FileCache(3) User Contributed Perl DocumentationBio::DB::FileCache(3)NAMEBio::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:
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
perl v5.14.1 2011-07-22 Bio::DB::FileCache(3)