Bio::G...tureDir(3pm)

💖 NAME 💖

Bio::Graphics::FeatureDir — it's literally a whole directory of feature files and conf files, bestie. Like a little folder that's got main character energy 🎀

(also hi, this is the manual page for Bio::Graphics::FeatureDir(3pm), from the User Contributed Perl Documentation, and it's giving iconic)

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✨ 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');

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🦋 DESCRIPTION 🦋

Okay so this class? It implements most of the methods of Bio::Graphics::FeatureFile, but instead of just vibing with everything in one place, it stores the data files and features in a directory indexed by the Bio::DB::SeqFeature::Store::berkeleydb adaptor. And because of that… it's fast. No cap. ⚡

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🌸 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 directory you pointed at. And bestie, it's not just the -dir directory argument — it also takes any of the options you could pass to Bio::Graphics::FeatureFile, except for the -file and -text arguments. Those two? Not invited. 🙅♀️

• $db->_init_featuredb — Internal method, iykyk. It initializes the underlying feature database. You don't call this one yourself, it's the behind-the-scenes bestie.
• $db->_init_conf — Another internal method — this one initializes the configuration file(s). ✨
• $created = $db->_maybe_create_dir($dir) — Creates $dir and all its parents if it doesn't already exist. Returns true if the directory got created. And heads up: it throws an exception on filesystem errors. 💀
• $dir = $db->dir — Returns the base directory. Simple, iconic, we love her.
• $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. It can add files of type .fa, .gff, .gff3, .conf and .ff. Periodt. 💅
• $db->add_fh(\*FILEHANDLE [,'name']) — Add the contents of the indicated filehandle to the repository. The name is optional; if you do provide it, it'll be used as the base for all files created. 🫶

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👑 SEE ALSO 👑

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

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🎀 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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😭 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'

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ngl bestie, even the docs had a little stumble, and honestly? Relatable. 🙈

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and that's a wrap, angel 💖 this page came to you from perl v5.30.0, dated 2019-11-25, stay slaying, go read some features ✨