Bio::C...age::IO(3pm)

💖 Bio::CodonUsage::IO — the Perl doc, bestie edition 💖

okay so real quick: this is Bio::C...age::IO(3pm), one of those User Contributed Perl Documentation pages, and it is genuinely the little IO goblin that reads and writes codon usage tables. let's get into it ✨

---

🌸 NAME 🌸

Bio::CodonUsage::IO — for reading and writing codon usage tables to file

---

✨ SYNOPSIS ✨

use Bio::CodonUsage::IO;

## read in a codon usage file
my $io = Bio::CodonUsage::IO->new(-file => "in");
my $cut = $io->next_data();

## write it out again
my $out = Bio::CodonUsage::IO->new(-file => ">out");
$out->write_data($cut);

---

🦋 DESCRIPTION 🦋

so this class is literally just giving you the standard IO methods for reading and writing text files full of codon usage tables. no cap. 🫶

those tables can initially be retrieved using Bio::DB::CUTG — that's where they come from, that's the source, periodt.

at present only this format is supported for read/write. that's it. that's the format. don't come for me about other formats, they are not here. 💅

and the cute part: reading a CUTG will return a Bio::CodonUsage::Table object. you give it a file, it hands you a whole object. main character energy honestly. 👑

---

🌈 SEE ALSO 🌈

• Bio::Tools::CodonTable
• Bio::WebAgent
• Bio::CodonUsage::Table
• Bio::CodonUsage::IO

(yes, the module sees itself. iconic behaviour. self-love fr fr. 💜)

---

💌 FEEDBACK 💌

📬 Mailing Lists 📬

user feedback is an integral part of the evolution of this and other Bioperl modules — like, the whole thing grows because y'all talk to us. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, genuinely 😭💖

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫶 Support 🫶

please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. the reason is that many experienced and responsive experts will be able look at the problem and quickly address it. if at all possible, please include a thorough description of the problem with code and data examples. give them the whole picture bestie, they'll eat it up. ✨

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

---

👑 AUTHORS 👑

Richard Adams, Richard.Adams@ed.ac.uk

---

📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — so if you see that underscore, mind your business, that's the private zone 🙈

🔧 new

Title  : new
Usage  : my $io = Bio::CodonUsage::IO->new(-file => "CUTfile");
Purpose: To  read/write a Bio:CodonUsage::Table object
Returns: A  Bio:CodonUsage::IO object
Args   : a file or file handle

so you call new, you hand it a file or a file handle, and it blesses you with a Bio:CodonUsage::IO object so you can read/write a Bio:CodonUsage::Table. that's the whole vibe check. ✅

🔧 next_data

Title  : next_data
Usage  : my $cut = $io->next_data();
Purpose: To  obtain a Bio:CodonUsage::Table object
Returns: A  Bio:CodonUsage::Table object
Args   : none

no args, no problem — it just hands you a Bio:CodonUsage::Table object. lowkey the easiest method on this whole page. 🎀

🔧 write_data

Title  : write_data
Usage  : $io->write_data($cut);
Purpose: To  write a CUT to file
Returns: void
Args   : a Bio::CodonUsage::Table object reference

you give it a Bio::CodonUsage::Table object reference and it writes that CUT to file. returns void, so like, don't go looking for a return value, there isn't one. it ate and left no crumbs and also left no return value. 💀

---

friendly reminder bestie: internal methods usually start with _, so if it's got the underscore it's not for you, it's for the module's own business. respect the boundary, it's giving healthy relationships 💜

---

and that's the whole page!! this was Bio::C...age::IO(3pm) from the User Contributed Perl Documentation, sitting pretty in perl v5.32.1, dated 2021-08-15. go read some codon usage tables, bestie, you got this 💅✨🌸🦋💖