Bio::DB::Flat(3) User Contributed Perl Documentation Bio::DB::Flat(3)NAMEBio::DB::Flat - Interface for indexed flat files
SYNOPSIS
$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('BUM');
@sequences = $db->get_Seq_by_acc('DIV' => 'primate');
$raw = $db->fetch_raw('BUM');
DESCRIPTION
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.
FEEDBACK
Mailing Lists
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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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/
AUTHOR - Lincoln Stein
Email - lstein@cshl.org
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with an "_" (underscore).
new
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.
new_from_registry
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.
fetch
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.
To Be Implemented in Subclasses
The following methods MUST be implemented by subclasses.
May Be Overridden in Subclasses
The following methods MAY be overridden by subclasses.
perl v5.14.1 2011-07-22 Bio::DB::Flat(3)