Bio::T...::Gene(3pm)

🧬 NAME 🧬

Bio::Tools::Prediction::Gene — a predicted gene structure feature 💖

Like, this is the whole vibe of Bio::T...::Gene(3pm) from the Bioperl Perl docs (User Contributed Perl Documentation, iykyk) — bestie, we're getting into predicted genes today 🎀

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✨ SYNOPSIS ✨

#See documentation of methods.

That's it. That's the synopsis. She's mysterious. She's giving "read the docs, babe." 💅

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🌸 DESCRIPTION 🌸

Okay so — this is a feature that represents a predicted gene structure. And the way that it actually inherits off Bio::SeqFeature::Gene::Transcript?? Iconic. Which means it comes with all of that functionality, plus a few extra methods that support predicted sequence features, like a predicted CDS and a predicted translation 🧚

The exons held by an instance of this class will usually be instances of Bio::Tools::Prediction::Exon, though lowkey they do not have to be. Go check the documentation of the class that produced the instance, fr fr.

Heads up bestie: normally you will not want to create an instance of this class yourself. Instead, classes representing the results of gene structure prediction programs will do that for you. Let them cook 👑

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💌 FEEDBACK 💌

Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated 🫶

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. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. (Yes, the original says "reponsive" — we keep it, it's part of the lore 😭)

Reporting Bugs 🐛

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

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

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👑 AUTHOR - Hilmar Lapp 👑

Email hlapp-at-gmx.net or hilmar.lapp-at-pharma.novartis.com

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (that underscore is a little secret handshake, iykyk ✨).

predicted_cds 🧬

• Title: predicted_cds
• Usage:

$predicted_cds_dna = $gene->predicted_cds();
$gene->predicted_cds($predicted_cds_dna);

• Function: Get/Set the CDS (coding sequence) as predicted by a program.

This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. 👀 Like, zero promises, bestie. Don't come for her if they don't match.

• Example: (none given, she's keeping it lowkey)
• Returns: A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program.
• Args: On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program.

predicted_protein 🌈

• Title: predicted_protein
• Usage:

$predicted_protein_seq = $gene->predicted_protein();
$gene->predicted_protein($predicted_protein_seq);

• Function: Get/Set the protein translation as predicted by a program.

This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. 💀 So like… usually fine, but no cap, no guarantees.

• Example: (also empty, mysterious queen)
• Returns: A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program.
• Args: On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program.

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And that's the whole page, bestie! ✨

This was Bio::T...::Gene(3pm) from perl v5.32.1, dated 2021-08-15 — mwah, slay, ate, no crumbs left 💅🎀💖