Bio::D...:memory(3pm)

💖 Bio::DB::GFF::Adaptor::memory 💖

okay so bestie, gather round — this is the manual page for Bio::DB::GFF::Adaptor::memory, part of the User Contributed Perl Documentation, and it's literally the in-memory database adaptor for Bio::DB::GFF. Think of it as the little gremlin that holds your whole genome in RAM. It's giving fast but smol. ✨

---

🌸 NAME 🌸

Bio::DB::GFF::Adaptor::memory — a Bio::DB::GFF database adaptor for in-memory databases. That's it, that's the whole job description. 💅

---

✨ SYNOPSIS ✨

Bestie you have two whole ways to do this. Pick your fighter:

Option one — the constructor does everything for you:

use Bio::DB::GFF;
my $db = Bio::DB::GFF->new(-adaptor=> 'memory',
                           -gff    => 'my_features.gff',
                           -fasta  => 'my_dna.fa'
                          );

or, option two — build it empty and load stuff in yourself:

my $db = Bio::DB::GFF->new(-adaptor=>'memory');
$db->load_gff_file('my_features.gff');
$db->load_fasta_file('my_dna.fa');

Also, if you wanna see the other methods, go look at Bio::DB::GFF. They're all inherited, she's the parent, respect her. 👑

---

🦋 DESCRIPTION 🦋

This adaptor implements an in-memory version of Bio::DB::GFF. What's it for? Storing and retrieving SHORT GFF files. Emphasis on SHORT, bestie, it says it in all caps for a reason. 🙈

It inherits from Bio::DB::GFF, so all that parent energy comes along for free. 💖

---

🎀 CONSTRUCTOR 🎀

Use Bio::DB::GFF->new() to construct new instances of this class. There are three named arguments that are recommended — here's the lineup:

• -adaptor — set it to "memory" and boom, you get an instance of this class. That's the whole vibe. ✨
• -gff — reads the indicated file, or a directory of .gff files. 🍓
• -fasta — reads the indicated file, or a directory of fasta files. 🧚
• -dir — points at a directory containing .gff and .fa files. 🎀

Okay but listen — if you use the -dir option and the directory it points to is writable by the current process, then this library will create a FASTA file index that greatly diminishes the memory usage of this module. Lowkey a glow-up for your RAM. 🔥

Alternatively — and this is the recommended path in CGI/mod_perl/fastCGI environments — you can make an empty in-memory object using just the -adaptor=>'memory' argument, and then call the load_gff_file() and load_fasta_file() methods to load GFF and/or sequence info.

Why though? Because those methods do not modify STDIN, unlike the constructor. No cap. If you're in a CGI-ish environment, that matters a LOT. 😭

---

💜 METHODS 💜

See Bio::DB::GFF for inherited methods. That's where the rest of the magic lives, bestie. ✨

---

💀 BUGS 💀

none ;-)

Not a single one. She said what she said. 😌💅

---

🌈 SEE ALSO 🌈

• Bio::DB::GFF
• bioperl

Go read those, they're iconic. 🫶

---

👑 AUTHOR 👑

Shuly Avraham <avraham@cshl.org>.

Copyright (c) 2002 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. Slay, honestly. 🌸

---

🌟 _feature_by_name 🌟

• Title — _feature_by_name
• Usage — $db->get_features_by_name($name,$class,$callback)
• Function — get a list of features by name and class
• Returns — count of number of features retrieved
• Args — name of feature, class of feature, and a callback
• Status — protected 🔒

This method is used internally — it's not for you to poke at, bestie, it's private business. 🙈 The callback arguments are those used by make_feature().

---

And that's the whole page, mwah. This lil doc came to you from perl v5.30.0 and it was dated 2020-01-13 — so go forth and load your short GFF files in memory, main character. Periodt. 💖✨🎀