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

💖 Bio::T...::Exon 💖

okay so bestie, welcome to the Bio::Tools::Sim4::Exon page from the User Contributed Perl Documentation, and no cap, it's giving iconic little exon energy. grab a strawberry 🍓, we're going in.

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✨ NAME ✨

Bio::Tools::Sim4::Exon — literally just a single exon determined by an alignment. that's her. that's the whole vibe. 🧬✨

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🌸 SYNOPSIS 🌸

# See Bio::Tools::Sim4::Results for a description of the context.

# an instance of this class is-a Bio::SeqFeature::SimilarityPair

# coordinates of the exon (recommended way):
print "exon from ", $exon->start(),
      " to ", $exon->end(), "\n";

# the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
print "exon from ", $exon->feature1()->start(),
      " to ", $exon->feature1()->end(), "\n";
# also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
print "exon from ", $exon->query()->start(),
      " to ", $exon->query()->end(), "\n";

# coordinates on the matching EST (recommended way):
print "matches on EST from ", $exon->est_hit()->start(),
      " to ", $exon->est_hit()->end(), "\n";

# the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
print "matches on EST from ", $exon->feature2()->start(),
      " to ", $exon->feature2()->end(), "\n";
# also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
print "exon from ", $exon->subject()->start(),
      " to ", $exon->subject()->end(), "\n";

the way that you can grab the same coordinates like four different ways?? multiple paths to the same slay, we love a flexible queen 👑💅

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🦋 DESCRIPTION 🦋

so this class inherits from Bio::SeqFeature::SimilarityPair and it represents an exon on a genomic sequence determined by similarity — aka by aligning an EST sequence (using Sim4 in this case, iykyk). so the whole notion of query and subject is always from the perspective of the genomic sequence: query = the genomic seq, subject = the aligned EST hit. because of this, $exon->start(), $exon->end() etc will always return what you expect. no surprises, no chaos, just correct coordinates. periodt. 💖

to get the coordinates on the matching EST, refer to the properties of the feature returned by est_hit(). 🫶

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💌 FEEDBACK 💌

🌈 Mailing Lists 🌈

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. 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. the more deets you give, the faster they can help you out bestie 🙈✨

🐛 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

not me telling you to file a real issue instead of vagueposting about it 💀 the maintainers will literally thank you.

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👑 AUTHOR - Ewan Birney, Hilmar Lapp 👑

Ewan Birney <birney-at-sanger.ac.uk> Hilmar Lapp <hlapp-at-gmx.net> or <hilmar.lapp-at-pharma.novartis.com>.

two legends, one module. we stan 🫶🌟

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📖 APPENDIX 📖

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

💜 percentage_id 💜

Title   : percentage_id
Usage   : $obj->percentage_id($newval)
Function: This is a synonym for 100 * $obj->est_hit()->frac_identical().
Returns : value of percentage_id
Args    : newvalue (optional)

so it's literally just a lil synonym for 100 * $obj->est_hit()->frac_identical(). math but make it cute ✨ pass in a $newval if you want (optional bestie, no pressure).

💜 est_hit 💜

Title   : est_hit
Usage   : $est_feature = $obj->est_hit();
Function: Returns the EST hit pointing to (i.e., aligned to by Sim4) this
          exon (i.e., genomic region). At present, merely a synonym for
          $obj->feature2().
Returns : An Bio::SeqFeatureI implementing object.
Args    :

returns the EST hit pointing to (i.e., aligned to by Sim4) this exon (i.e., genomic region). at present, merely a synonym for $obj->feature2(). returns an Bio::SeqFeatureI implementing object. args? none, she takes no arguments, she's low maintenance 💅

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and that's the whole page bestie!! 💖✨🎀🦋🌸🫶

this lil masterpiece is documented for perl v5.32.1 and dated 2021-08-15. go forth and align some exons, you absolute main character 👑💜