Bio::DB FileCache
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Summary
Bio::DB::FileCache - In file cache for BioSeq objects
Package variables
No package variables defined.
Included modules
Bio::Annotation::Collection
Bio::Location::Fuzzy
Bio::Location::Split
Bio::Seq
Bio::Seq::RichSeq
Bio::SeqFeature::Generic
Bio::Species
DB_File
Fcntl qw ( O_CREAT O_RDWR O_RDONLY )
File::Temp ' tmpnam '
Storable qw ( freeze thaw )
Inherit
Bio::DB::SeqI Bio::Root::Root
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, );
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.
Methods
newDescriptionCode
get_Seq_by_idDescriptionCode
get_Seq_by_accDescriptionCode
seqdbDescriptionCode
file_nameDescriptionCode
keepDescriptionCode
dbDescriptionCode
flushDescriptionCode
_get
No description
Code
_store
No description
Code
get_Seq_by_versionDescriptionCode
DESTROY
No description
Code
_open_database
No description
Code
Methods description
newcode    nextTop
 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_idcodeprevnextTop
 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_acccodeprevnextTop
 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
seqdbcodeprevnextTop
 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_namecodeprevnextTop
 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.
keepcodeprevnextTop
 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.
dbcodeprevnextTop
 Title   : db
Usage : $db->db
Function: returns tied hash to index database
Returns : a Berkeley DB tied hashref
Args : none
Throws : nothing
flushcodeprevnextTop
 Title   : flush
Usage : $db->flush
Function: flushes the cache
Returns : nothing
Args : none
Throws : nothing
get_Seq_by_versioncodeprevnextTop
 Title   : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
Methods code
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;

    my $self = Bio::Root::Root->new();
    bless $self,$class;

    my ($seqdb,$file_name,$keep) = $self->_rearrange([qw(SEQDB FILE
							 KEEP)],@args);

    if( !defined $seqdb || !ref $seqdb ||
	! $seqdb->isa('Bio::DB::RandomAccessI') ) {
       $self->throw("Must be a randomaccess database not a [$seqdb]");
    }

    $self->seqdb($seqdb);
    $file_name ||= tmpnam();
    $self->file_name($file_name);
    $self->keep($keep);

    $self->_open_database($file_name);
    return $self;
}
get_Seq_by_iddescriptionprevnextTop
sub get_Seq_by_id {
   my ($self,$id) = @_;

   # look in the cache first
my $obj = $self->_get('id' => $id); return $obj if defined $obj; # get object from seqdb
$obj = $self->seqdb->get_Seq_by_id($id); $self->_store('id' => $id, $obj); return $obj;
}
get_Seq_by_accdescriptionprevnextTop
sub get_Seq_by_acc {
   my ($self,$acc) = @_;

   # look in the cache first
my $obj = $self->_get('acc' => $acc); return $obj if defined $obj; # get object from seqdb
$obj = $self->seqdb->get_Seq_by_acc($acc); $self->_store('acc' => $acc, $obj); return $obj;
}
seqdbdescriptionprevnextTop
sub seqdb {
    my ($self, $seqdb) = @_;
    if ($seqdb) {
        $self->{'seqdb'} = $seqdb;
    } else {
        return $self->{'seqdb'};
    }
}
file_namedescriptionprevnextTop
sub file_name {
  my $self = shift;
  my $d = $self->{file_name};
  $self->{file_name} = shift if @_;
  $d;
}
keepdescriptionprevnextTop
sub keep {
  my $self = shift;
  my $d = $self->{keep};
  $self->{keep} = shift if @_;
  $d;
}
dbdescriptionprevnextTop
sub db {
 shift->{db}
}
flushdescriptionprevnextTop
sub flush {
  my $db = shift->db or return;
  %{$db} = ();
}
_getdescriptionprevnextTop
sub _get {
  my $self = shift;
  my ($type,$id) = @_;
  my $serialized = $self->db->{"${type}_${id}"};
  my $obj = thaw($serialized);
  $obj;
}
_storedescriptionprevnextTop
sub _store {
  my $self = shift;
  my ($type,$id,$obj) = @_;
  if( ! defined $obj ) {
      # bug #1628
$self->debug("tried to store an undefined value for $id, skipping"); return; } my $serialized = freeze($obj); $self->db->{"${type}_${id}"} = $serialized;
}
get_Seq_by_versiondescriptionprevnextTop
sub get_Seq_by_version {
   my ($self,@args) = @_;
   $self->throw("Not implemented it");
}
DESTROYdescriptionprevnextTop
sub DESTROY {
  my $self = shift;
  unlink $self->file_name unless $self->keep;
}
_open_databasedescriptionprevnextTop
sub _open_database {
  my $self = shift;
  my $file = shift;
  my $flags = O_CREAT|O_RDWR;
  my %db;
  tie(%db,'DB_File',$file,$flags,0666,$DB_BTREE)
    or $self->throw("Could not open primary index file");
  $self->{db} =\% db;
  unlink $file unless $self->keep;
}

## End of Package
1;
}
General documentation
CONTACTTop
Lincoln Stein <lstein@cshl.org>
Support Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _