Bio::S...criptI(3pm)

💖 Bio::SeqFeature::Gene::TranscriptI 💖

okay bestie, come closer — this is the manual page for Bio::SeqFeature::Gene::TranscriptI (you'll see it chilling in the header as Bio::S...criptI(3pm) because the terminal column was NOT about to give it the space it deserved, and honestly, relatable).

It lives in the User Contributed Perl Documentation collection. Pull up a chair, grab a strawberry 🍓, and let's get into it.

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✨ NAME ✨

Bio::SeqFeature::Gene::TranscriptI — the Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.

(yes it's an interface, not a class — it's giving "I define the vibe, you implement the vibes" 💅)

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🌸 SYNOPSIS 🌸

  #documentation needed

not me showing you a synopsis that is literally just a comment saying the docs are missing 😭 iconic honestly. The canon is the canon, we don't invent code that isn't there.

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🦋 DESCRIPTION 🦋

A feature representing a transcript.

That's it. That's the description. Short, sweet, main character energy, says exactly one (1) true thing. 👑

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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.

(translation: don't DM the maintainer, post to the list, and bring receipts — code AND data examples, bestie. The experts eat that up.)

💀 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

fr fr, file it on the tracker so it doesn't get lost in the void 🕳️

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🧚 AUTHOR - Hilmar Lapp 🧚

Email hlapp@gmx.net

shoutout to the author, no cap 🫡

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

iykyk — the _ prefix means "internal, don't touch unless you know what you're doing".

🎀 promoters

• Title — promoters()
• Usage —

  @proms = $transcript->promoters();

• Function — Get the promoter features of this transcript.

Note that OO-modeling of regulatory elements is not stable yet. This means that this method might change or even disappear in a future release. Be aware of this if you use it.

• Returns — An array of Bio::SeqFeatureI implementing objects representing the promoter regions or sites.
• Args —

⚠️ heads up bestie: the OO-modeling of regulatory elements is NOT stable yet. This method might change or even straight up disappear in a future release. Be aware of this if you use it. ⚠️

🧬 exons

• Title — exons()
• Usage —

  @exons = $transcript->exons();
  @inital = $transcript->exons('Initial');

• Function — Get the individual exons this transcript comprises of, or all exons of a specified type.

Refer to the documentation of the class that produced this transcript object for information about the possible types.

See Bio::SeqFeature::Gene::ExonI for properties of the returned objects.

• Returns — An array of Bio::SeqFeature::Gene::ExonI implementing objects
• Args — An optional string specifying the type of the exon.

🌸 introns

• Title — introns()
• Usage —

  @introns = $transcript->introns();

• Function — Get all introns this transcript comprises of.
• Returns — An array of Bio::SeqFeatureI implementing objects representing the introns.
• Args —

🍓 poly_A_site

• Title — poly_A_site()
• Usage —

  $polyAsite = $transcript->poly_A_site();

• Function — Get the poly-adenylation site of this transcript.
• Returns — A Bio::SeqFeatureI implementing object.
• Args —

✨ utrs

• Title — utrs()
• Usage —

  @utr_sites = $transcript->utrs();

• Function — Get the UTR regions this transcript comprises of.

See Bio::SeqFeature::Gene::ExonI for properties of the returned objects.

• Returns — An array of Bio::SeqFeature::Gene::ExonI implementing objects
• Args —

💜 mrna

• Title — mrna()
• Usage —

  $mrna = $transcript->mrna();

• Function — Get the mRNA of the transcript as a sequence object.
• Returns — A Bio::PrimarySeqI implementing object.
• Args —

🔥 cds

• Title — cds()
• Usage —

  $cds = $transcript->cds();

• Function — Get the CDS (coding sequence) of the transcript as a sequence object.
• Returns — A Bio::PrimarySeqI implementing object.
• Args —

👑 protein

• Title — protein()
• Usage —

  $protein = $transcript->protein();

• Function — Get the protein encoded by the transcript as a sequence object.
• Returns — A Bio::PrimarySeqI implementing object.
• Args —

🌈 parent

• Title — parent
• Usage —

  $obj->parent($newval)

• Function — get the parent gene of the transcript
• Returns — value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
• Args — a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)

(yep, the arg is optional — call it with no args to just peek at the parent, call it with an object to set the parent. get/set duality, we love to see it 💅)

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and that's the whole page, bestie 🎀

This one shipped with perl v5.32.1, dated 2021-08-15, and answers to the name Bio::S...criptI(3pm) in the manual. Go forth and annotate some transcripts. slay 💖✨🦋