Bio::DB::Flat - Interface for indexed flat files
$db = Bio::DB::Flat->new(-directory => '/usr/share/embl',
-dbname => 'mydb',
-format => 'embl',
-index => 'bdb',
-write_flag => 1);
$db->build_index('/usr/share/embl/primate.embl',
'/usr/share/embl/protists.embl');
$seq = $db->get_Seq_by_id('HSFOS');
@sequences = $db->get_Seq_by_acc('DIV' => 'primate');
$raw = $db->fetch_raw('HSFOS');
This object provides the basic mechanism to associate positions in files with
primary and secondary name spaces. Unlike Bio::Index::Abstract (see
Bio::Index::Abstract), this is specialized to work with the "flat
index" and BerkeleyDB indexed flat file formats worked out at the 2002
BioHackathon.
This object is a general front end to the underlying databases.
User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to one of the Bioperl
mailing lists. Your participation is much appreciated.
[email protected] - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
[email protected]
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.
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
Email -
[email protected]
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with an "_" (underscore).
Title : new
Usage : my $db = Bio::DB::Flat->new(
-directory => $root_directory,
-dbname => 'mydb',
-write_flag => 1,
-index => 'bdb',
-verbose => 0,
-out => 'outputfile',
-format => 'genbank');
Function: create a new Bio::DB::Flat object
Returns : new Bio::DB::Flat object
Args : -directory Root directory containing "config.dat"
-write_flag If true, allows creation/updating.
-verbose Verbose messages
-out File to write to when write_seq invoked
-index 'bdb' or 'binarysearch'
Status : Public
The required -directory argument indicates where the flat file indexes will be
stored. The
build_index() and
write_seq() methods will
automatically create subdirectories of this root directory. Each subdirectory
will contain a human-readable configuration file named "config.dat"
that specifies where the individual indexes are stored.
The required -dbname argument gives a name to the database index. The index
files will actually be stored in a like-named subdirectory underneath the root
directory.
The -write_flag enables writing new entries into the database as well as the
creation of the indexes. By default the indexes will be opened read only.
-index is one of "bdb" or "binarysearch" and indicates the
type of index to generate. "bdb" corresponds to Berkeley DB. You
*must* be using BerkeleyDB version 2 or higher, and have the Perl BerkeleyDB
extension installed (DB_File will *not* work). "binarysearch"
corresponds to the OBDA "flat" indexed file.
The -out argument specifies the output file for writing objects created with
write_seq().
The -format argument specifies the format of the input file or files. If the
file suffix is one that Bioperl can already associate with a format then this
is optional.
Title : new_from_registry
Usage : $db = Bio::DB::Flat->new_from_registry(%config)
Function: creates a new Bio::DB::Flat object in a Bio::DB::Registry-
compatible fashion
Returns : new Bio::DB::Flat
Args : provided by the registry, see below
Status : Public
The following registry-configuration tags are recognized:
location Root of the indexed flat file; corresponds to the new() method's
-directory argument.
Title : fetch
Usage : $index->fetch( $id )
Function: Returns a Bio::Seq object from the index
Example : $seq = $index->fetch( 'dJ67B12' )
Returns : Bio::Seq object
Args : ID
Deprecated. Use get_Seq_by_id instead.
The following methods MUST be implemented by subclasses.
The following methods MAY be overridden by subclasses.