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Bio::Graphics::FeatureUser3Contributed Perl DocumeBio::Graphics::FeatureDir(3)

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.

POD ERRORS
       Hey! The	above document had some	coding errors, which are explained
       below:

       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'

perl v5.32.0			  2020-08-29	  Bio::Graphics::FeatureDir(3)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | AUTHOR | POD ERRORS

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