Lincoln D. Stein > Bio-Graphics-2.31 > Bio::Graphics::FeatureDir

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Source   Latest Release: Bio-Graphics-2.37

NAME ^

Bio::Graphics::FeatureDir -- A directory of feature files and conf files

SYNOPSIS ^

 my $fd = Bio::Graphics::FeatureDir->new('/path/to/dir');
 $fd->add_file('tracks.conf');
 $fd->add_file('foo.gff3');
 $fd->add_file('foo.wig');
 $fd->add_fh(\*STDIN);
 
 my $option   = $fd->setting('EST' => 'bgcolor');
 my @features = $fd->get_features_by_name('M101');

DESCRIPTION ^

This class implements most of the methods of Bio::Graphics::FeatureFile, but stores the data files and features in a directory indexed by the Bio::DB::SeqFeature::Store::berkeleydb adaptor. Therefore it is fast.

Methods

$fd = Bio::Graphics::FeatureDir->new('/path/to/dir');
$fd = Bio::Graphics::FeatureDir->new(-dir => '/path/to/dir');

Create a new FeatureDir, based in the indicated directory. In addition to the -dir directory argument, it takes any of the options that can be passed to Bio::Graphics::FeatureFile except for the -file and -text arguments;

$db->_init_featuredb

Internal method. Initializes the underlying feature database.

$db->_init_conf

Internal method -- initialize the configuration file(s)

$created = $db->_maybe_create_dir($dir)

Create $dir and its parents if it doesn't exist. Return true if the directory was created. Throws an exception on filesystem errors.

$dir = $db->dir

Returns the base directory.

$conf = $db->conf

Returns the underlying Bio::Graphics::FeatureFile object

$db = $db->db

Returns the underlying Bio::DB::SeqFeature::Store object

$db->add_file($file)

Add the file to the directory. Can add files of type .fa, .gff, .gff3, .conf and .ff.

$db->add_fh(\*FILEHANDLE [,'name'])

Add the contents of the indicated filehandle to repository. Name is optional; if provided it will be used as the base for all files created.

SEE ALSO ^

Bio::Graphics::Feature, Bio::Graphics::FeatureFile

AUTHOR ^

Lincoln Stein <lincoln.stein@gmail.com>.

Copyright (c) 2009 Ontario Institute for Cancer Research

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.

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