Bio::S...e::Exon(3pm)

💖 NAME 💖

okay so welcome to Bio::S...e::Exon(3pm) bestie — yes that's the manual name, it's giving "shy about the middle of my own module path" energy, we love her anyway 🎀

Bio::SeqFeature::Gene::Exon — a feature representing an exon. that's the whole job description. she's an exon. she contains multitudes. ✨

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🦋 SYNOPSIS 🦋

like, imagine you already have an exon instance somehow (manifesting one for you rn) and then you just:

# obtain an exon instance $exon somehow
print "exon from ", $exon->start(), " to ", $exon->end(),
      " on seq ", $exon->seq_id(), ", strand ", $exon->strand(),
      ", encodes the peptide sequence ",
      $exon->cds()->translate()->seq(), "\n";

and boom, she's telling you her whole life story. iconic. no cap. 💅

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🌸 DESCRIPTION 🌸

This module implements a feature representing an exon by implementing the Bio::SeqFeature::Gene::ExonI interface. so yes, she's got interfaces, she's got range, she's a whole main character.

By default an Exon is coding. fr fr, that's the default setting. if you want her to be a non-coding girlie, supply -is_coding => 0 to the constructor, or just call $exon->is_coding(0) otherwise. your call, bestie, both paths slay. 🫶

Apart from that, this class also implements Bio::SeqFeatureI by inheriting off Bio::SeqFeature::Generic. so she's not just an exon, she's also a whole sequence feature. multi-talented. ate. 🔥

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📬 FEEDBACK 📬

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. (translation: they literally cannot glow up without you 💖). Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. like, 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 reponsive experts will be able look at the problem and quickly address it — a whole group chat of geniuses, basically. 👑

Please include a thorough description of the problem with code and data examples if at all possible. no vague "it's broken" texts please, give them the receipts 🧾✨

🐛 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

go off, file that issue, you're doing the community a service 🌈

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👑 AUTHOR - Hilmar Lapp 👑

Email hlapp@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, that underscore is the "do not perceive me" marker 🙈).

🧬 is_coding

• Title — is_coding
• Usage —

if($exon->is_coding()) {
        # do something
}
if($is_utr) {
    $exon->is_coding(0);
}

• Function — Get/set whether or not the exon codes for amino acid.
• Returns — TRUE if the object represents a feature translated into protein, and FALSE otherwise.
• Args — A boolean value on set.

🏷️ primary_tag

• Title — primary_tag
• Usage —

$tag = $feat->primary_tag()
$feat->primary_tag('exon')

• Function — Get/set the primary tag for the exon feature.

This method is overridden here in order to allow only for tag values following a certain convention. For consistency reasons, the tag value must either contain the string 'exon' or the string 'utr' (both case-insensitive). In the case of 'exon', a string describing the type of exon may be appended or prefixed. Presently, the following types are allowed: initial, internal, and terminal (all case-insensitive).

If the supplied tag value matches 'utr' (case-insensitive), is_coding() will automatically be set to FALSE, and to TRUE otherwise. (yes she updates her own vibe check, self-sufficient queen 💅)

• Returns — A string.
• Args — A string on set.

📍 location

• Title — location
• Usage —

my $location = $exon->location()

• Function — Returns a location object suitable for identifying the location of the exon on the sequence or parent feature.

This method is overridden here to restrict allowed location types to non-compound locations. (compound locations? not invited to this party 🚫)

• Returns — Bio::LocationI object
• Args — none

🍓 cds

• Title — cds()
• Usage —

$cds = $exon->cds();

• Function — Get the coding sequence of the exon as a sequence object.

The sequence of the returned object is prefixed by Ns (lower case) if the frame of the exon is defined and different from zero. The result is that the first base starts a codon (frame 0). she's lining up her bases so the reading frame makes sense, so thoughtful ✨

This implementation returns undef if the particular exon is not translated to protein, i.e., is_coding() returns FALSE. undef will also be returned if no sequence is attached to this exon feature. (no sequence, no cds, she said respectfully 🙈)

• Returns — A Bio::PrimarySeqI implementing object.
• Args —

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okay that's the whole page bestie, you read all of it, I'm so proud 🥹💜 this came from User Contributed Perl Documentation, perl v5.32.1, dated 2021-08-15, and it's Bio::S...e::Exon(3pm) — go forth and annotate your exons, periodt 🌈⭐