Bio::Graphics::FeatureDir3pm

Usage

 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');

Overview

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.

Pod errors

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`Around line 160:`	'=item' outside of any '=over'
`Around line 272:`	=cut found outside a pod block. Skipping to next block.
`Around line 274:`	You forgot a '=back' before '=head1'

Releases

8 releases since Debian 6.0 (Squeeze); the text changed 5 times.

6.0
7
8
9
10
11–13