Bio::Graphics::FeatureUser3Contributed Perl DocumeBio::Graphics::FeatureDir(3)NAMEBio::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 161:
'=item' outside of any '=over'
Around line 273:
=cut found outside a pod block. Skipping to next block.
Around line 275:
You forgot a '=back' before '=head1'
perl v5.14.1 2011-07-22 Bio::Graphics::FeatureDir(3)
