RG::Reprof(3pm)

✨ NAME ✨

RG::Reprof::Reprof — it's a protein secondary structure and accessibility predictor, bestie 💖 (and yeah, the whole page lives in the RG::Reprof(3pm) man page, Perl's user contributed docs section, iykyk)

---

🌸 SYNOPSIS 🌸

use RG::Reprof::Reprof;

That's it, that's the whole vibe check. Load it and you're in 🫶

---

🦋 DESCRIPTION 🦋

Okay so real talk: the actual tea is in the module's commented source. See module commented source for further details. That's the official word, and I'm not gonna invent lore that isn't there 💅

💅 Methods

OBJ RG::Reprof::Reprof->new( model_dir => PATH )

Hiii this is the constructor, the main character moment ✨

• Default model_dir: /tmp/lkajan/root/share/reprof.

Returns a shiny new instance of RG::Reprof::Reprof. Obsessed 😌

int $OBJ->run( input_file => PATH, out_file => PATH, mutation_file => PATH, specific_models => hashref, output_func => coderef )

This is the one that actually does the thing 🔥 Note the details, bestie:

• out_file may be a directory. 👀 (yes, a directory, it's giving flexible)
• mutation_file may be undefined.
• specific_models may be undefined.

When specific_models is defined, it's a hash of model and feature files with 'model_name' keys, like this:

{
  'fub_model' => '/path/to/model_file',
  'fub_features' => '/path/to/features_file'
}

Check the module source for the list for model names. 👑 (fr fr, I can't hand you a list that isn't in the source)

void output_func( out_file, sec_pred, acc_pred, sequence ) — function to call when output is ready

If it's undefined, the built-in write_output() function gets called instead, which prints results to one or more files. 🎀

The following positional parameters are passed to this function:

• out_file — Output file name.
• sec_pred — Secondary structure prediction, see source for details.
• acc_pred — Accessibility prediction, see source for details.
• sequence — Reference to array of residues of input sequence (e.g. [ 'M', 'A', 'G', ... ] ).

---

🌈 AUTHOR 🌈

Original version by Peter Hoenigschmid <hoenigschmid@rostlab.org> and Burkhard Rost.

Some perl module work and documentation by Laszlo Kajan <lkajan@rostlab.org>.

Shoutout to the legends, no cap 🫡💜

---

🧚 SEE ALSO 🧚

• <http://rostlab.org/>

---

And that's the whole page, bestie! This little gem is from perl v5.32.1, dated 2022-01-18, and it's the RG::Reprof(3pm) page — take care of it and it'll take care of your protein predictions 🦋✨💖