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

💖 Bio::SeqFeature::Gene::ExonI(3pm) 💖

okay bestie, welcome to the Bio::SeqFeature::Gene::ExonI page — it's the interface for a feature representing an exon, and yes it's a whole vibe. This is the manual page for Bio::S...:ExonI(3pm), and we're gonna get into it together. 🧚✨

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🌸 NAME 🌸

Bio::SeqFeature::Gene::ExonI — the interface for a feature that represents an exon. that's the whole job description, she's an interface, she's an exon, she's iconic. 💅

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✨ SYNOPSIS ✨

ngl the synopsis is giving "figure it out from the methods", because it literally just says:

See documentation of methods.

so like… scroll down to the APPENDIX, bestie, that's where the methods live. 🫶

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🦋 DESCRIPTION 🦋

so this is a feature representing an exon. and in this definition, an exon is transcribed and — at least for one particular transcript — it is not spliced out of the pre-mRNA. periodt. that's the definition, no notes.

but here's the plot twist: it does not necessarily code for amino acid. 😭 so like, don't assume. an exon can be out here living its best non-coding life.

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💌 FEEDBACK 💌

🌈 Mailing Lists

user feedback is, like, integral to the evolution of this and other Bioperl modules — no cap. so if you have comments or suggestions, pls pls pls send them to one of the Bioperl mailing lists. your participation is much appreciated, fr fr. 🥹

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

🫶 Support

okay so usage questions and support issues? send those to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, bestie. the reason is lowkey wholesome: there are lots of experienced, responsive experts on the list who can look at your problem and quickly address it. 👑

please include a thorough description of the problem, with code and data examples, if at all possible. the more detail the better, that's the whole vibe check. 💯

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. it's giving organized. it's giving responsible. we love to see it. ✨

bug reports can be submitted via the web:

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

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👑 AUTHOR - Hilmar Lapp 👑

email: hlapp@gmx.net

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📖 APPENDIX 📖

the rest of the documentation goes into the details of each of the object methods. heads up: internal methods are usually preceded with a _ — that's the little secret handshake, iykyk. 🙈

🧬 is_coding

Title   : is_coding
Usage   : if($exon->is_coding()) {
                  # do something
          }
Function: Whether or not the exon codes for amino acid.
Returns : TRUE if the object represents a feature translated into protein,
          and FALSE otherwise.
Args    :

so is_coding is the method you call when you need to know: does this exon code for amino acid or not? 🤔 it returns TRUE if the object represents a feature that gets translated into protein, and FALSE otherwise. args? none. she takes nothing. she just tells you. 💅

🎀 cds

Title   : cds()
Usage   : $cds = $exon->cds();
Function: Get the coding sequence of the exon as a sequence object.

          The returned sequence object must be in frame 0, i.e., the first
          base starts a codon.

          An implementation may return undef, indicating that a coding
          sequence does not exist, e.g. for a UTR (untranslated region).

Returns : A L<Bio::PrimarySeqI> implementing object.
Args    :

okay so cds() gets you the coding sequence of the exon as a sequence object. and there are rules, bestie:

• the returned sequence object must be in frame 0, meaning the first base starts a codon. no funny business. 🧬
• an implementation may return undef, which means a coding sequence does not exist — like for a UTR (untranslated region). so if you get undef, that's not a bug, that's just the situation. 😌

Returns: a Bio::PrimarySeqI implementing object.

Args: none, she's self-sufficient. 🦋

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lowkey reminder: this whole page is the interface docs, so an implementation might do its own thing within these rules — but the rules above? those are the rules. 🌟

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and that's the whole page, bestie!! thanks for reading, you ate. 💅✨

this gem was brought to you by perl v5.32.1, dated 2021-08-15, from Bio::S...:ExonI(3pm) — mwah, take care of her. 🎀💖🦋