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

💖 Bio::SeqFeature::Gene::GeneStructure 💖

okay bestie, welcome to Bio::SeqFeature::Gene::GeneStructure from the User Contributed Perl Documentation — she's giving Bioperl energy and she's literally the blueprint for a whole gene. no cap. 🧬✨

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🌸 NAME 🌸

Bio::SeqFeature::Gene::GeneStructure — a feature representing an arbitrarily complex structure of a gene. yes, arbitrarily complex. she contains multitudes. 👑

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✨ SYNOPSIS ✨

# See documentation of methods.

that's it. that's the synopsis. the methods are down in the APPENDIX, girlie, scroll. 💅

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🦋 DESCRIPTION 🦋

so this is a feature that represents a gene structure. and rn — as of now — a gene structure is really just a collection of transcripts. that's the whole vibe.

for the deets on what those transcript objects can actually do, go peek at:

• Bio::SeqFeature::Gene::TranscriptI — the interface 🎀
• Bio::SeqFeature::Gene::Transcript — the actual implementation 🌈

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is literally an integral part of the evolution of this and every other Bioperl module. so send your comments and suggestions — preferably to one of the Bioperl mailing lists. your participation is so appreciated, fr fr. 😭💖

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

🆘 Support

pls pls pls direct your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

...rather than sliding into the module maintainer's DMs directly. 🙈 there are so many experienced and responsive experts who will be able to look at your problem and quickly address it. and bestie — if at all possible, include a thorough description of the problem with code and data examples. the more context, the better. 🫶

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions. 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 ✨

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — iykyk. 💅

🌟 transcripts

• Title — transcripts
• Usage — @transcripts = $gene->transcripts();
• Function — get the transcripts of this gene structure. many gene structures will have only one transcript.
• Returns — an array of Bio::SeqFeature::Gene::TranscriptI implementing objects.
• Args — (none)

🌟 add_transcript

• Title — add_transcript()
• Usage — $gene->add_transcript($transcript);
• Function — add a transcript to this gene structure.
• Returns — (nothing)
• Args — a Bio::SeqFeature::Gene::TranscriptI implementing object.

🌟 flush_transcripts

• Title — flush_transcripts()
• Usage — $gene->flush_transcripts();
• Function — remove all transcripts from this gene structure. gone. poof. 💀
• Returns — (nothing)
• Args — (none)

🌟 add_transcript_as_features

• Title — add_transcript_as_features
• Usage — $gene->add_transcript_as_features(@featurelist);
• Function — take a list of Bio::SeqFeatureI objects and turn them into a Bio::SeqFeature::Gene::Transcript object. then add that transcript to the gene. ✨
• Returns — nothing
• Args — a list of Bio::SeqFeatureI compliant objects

🌟 promoters

• Title — promoters
• Usage — @prom_sites = $gene->promoters();
• Function — get the promoter features of this gene structure.

this method basically merges the promoters returned by transcripts.

⚠️ note that OO-modeling of regulatory elements is not stable yet. this means this method might change or even disappear in a future release. be aware of this if you use it, bestie. don't build your whole personality on it. 😭

• Returns — an array of Bio::SeqFeatureI implementing objects.
• Args — (none)

🌟 exons

• Title — exons()
• Usage —

@exons = $gene->exons();
@inital_exons = $gene->exons('Initial');

• Function — get all exon features, or all exons of a specified type, of this gene structure.

exon type is treated as a case-insensitive regular expression and is optional. for consistency, use only the following types: initial, internal, terminal, utr, utr5prime, and utr3prime. a special and virtual type is 'coding', which refers to all types except utr. 🧚

this method basically merges the exons returned by transcripts.

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

🌟 introns

• Title — introns()
• Usage — @introns = $gene->introns();
• Function — get all introns of this gene structure.

⚠️ note that this class currently generates these features on-the-fly — that is, it simply treats all regions between exons as introns. it assumes that the exons in the transcripts do not overlap. so like, don't come for her if your exons are messy. 💀

this method basically merges the introns returned by transcripts.

• Returns — an array of Bio::SeqFeatureI implementing objects.
• Args — (none)

🌟 poly_A_sites

• Title — poly_A_sites()
• Usage — @polyAsites = $gene->poly_A_sites();
• Function — get the poly-adenylation sites of this gene structure.

this method basically merges the poly-adenylation sites returned by transcripts.

• Returns — an array of Bio::SeqFeatureI implementing objects.
• Args — (none)

🌟 utrs

• Title — utrs()
• Usage —

@utr_sites = $gene->utrs('3prime');
@utr_sites = $gene->utrs('5prime');
@utr_sites = $gene->utrs();

• Function — get the features representing untranslated regions (UTR) of this gene structure.

you may provide an argument specifying the type of UTR. currently the following types are recognized: 5prime and 3prime for UTR on the 5' and 3' end of the CDS, respectively. 🌸

this method basically merges the UTRs returned by transcripts.

• Returns — an array of Bio::SeqFeature::Gene::ExonI implementing objects representing the UTR regions or sites.
• Args — optionally, either 3prime, or 5prime for the the type of UTR feature.

🌟 sub_SeqFeature

• Title — sub_SeqFeature
• Usage — @feats = $gene->sub_SeqFeature();
• Function — returns an array of all subfeatures.

this method is defined in Bio::SeqFeatureI. we override it here to include the transcripts. 👑

• Returns — an array of Bio::SeqFeatureI implementing objects.
• Args — none

🌟 flush_sub_SeqFeature

• Title — flush_sub_SeqFeature
• Usage —

$gene->flush_sub_SeqFeature();
$gene->flush_sub_SeqFeature(1);

• Function — removes all subfeatures.

⚠️ this method is overridden from Bio::SeqFeature::Generic to flush all additional subfeatures, i.e., transcripts — which is almost certainly not what you want. 😭 to remove only features added through $gene->add_sub_SeqFeature($feature), pass any argument evaluating to TRUE.

• Example — (none given)
• Returns — none
• Args — optionally, an argument evaluating to TRUE will suppress flushing of all gene structure-specific subfeatures (transcripts).

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perl v5.32.1 · 2021-08-15 · that's the whole page, bestie — go write some gene structures 💖🧬✨