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

💖 Bio::Tools::Spidey::Exon 💖

okay bestie, gather round, because we're talking about Bio::Tools::Spidey::Exon — the little Perl module from the Bio::T...::Exon(3pm) manpage that is literally one single exon determined by an alignment. one exon. she's a main character, she's small, she's powerful, she ate. 🧬✨

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✨ NAME ✨

Bio::Tools::Spidey::Exon — a single exon determined by an alignment. periodt. 💅

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🌸 SYNOPSIS 🌸

okay so here's the vibe check. the context is described over in Bio::Tools::Spidey::Results (go read that one, bestie 🫶).

an instance of this class is-a Bio::SeqFeature::SimilarityPair. got it? good.

# See Bio::Tools::Spidey::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";

like yes, there are three ways to say the same thing, and no, that's not a bug, that's inheritance being iconic 💀

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🦋 DESCRIPTION 🦋

So. This class inherits from Bio::SeqFeature::SimilarityPair and represents an exon on a genomic sequence determined by similarity — that is, by aligning an EST sequence (using Spidey, in this case). ✨

And here's the tea that makes everything make sense: the 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 cap. 🙌

To get the coordinates on the matching EST, refer to the properties of the feature returned by est_hit(). that's the move, bestie.

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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, fr fr 🌈

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. 👑

🐛 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

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👑 AUTHOR - Ryan Golhar 👑

Email golharam@umdnj.edu

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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
• Function: This is the percent id as reported by Spidey
• Returns: value of percentage_id
• Args: (none)

🧚 est_hit

• Title: est_hit
• Usage: $est_feature = $obj->est_hit();
• Function: Returns the EST hit pointing to (i.e., aligned to by Spidey) this exon (i.e., genomic region). At present, merely a synonym for $obj->feature2().
• Returns: An Bio::SeqFeatureI implementing object.
• Args: (none)

🌸 mismatches

• Title: mismatches
• Usage: $obj->mismatches;
• Function: Returns the mismatches of the cDNA to (i.e., aligned to by Spidey) this exon (i.e., genomic region).
• Returns: value of mismatches.
• Args: (none)

💜 gaps

• Title: gaps
• Usage: $obj->gaps;
• Function: Returns the gaps of the cDNA to (i.e., aligned to by Spidey) this exon (i.e., genomic region).
• Returns: value of gaps.
• Args: (none)

🍓 donor

• Title: donor
• Usage: $obj->donor;
• Function: Returns 0 if a splice donor site does not exist, or 1 if a splice donor site exists
• Returns: value of existence of donor splice site (0 or 1)
• Args: (none)

🌈 acceptor

• Title: acceptor
• Usage: $obj->acceptor;
• Function: Returns 0 if a splice acceptor site does not exist, or 1 if a splice acceptor site exists
• Returns: value of existence of acceptor splice site (0 or 1)
• Args: (none)

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okay that's the whole page, you're officially a Spidey exon expert, slay 💅✨ this one's from perl v5.32.1, dated 2021-08-15, and it lives in Bio::T...::Exon(3pm) — mwah, go read your alignments bestie 🫶🎀