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

💖 Bio::SeqFeature::SimilarityPair(3pm) 💖

okay bestie, so this page lives in the User Contributed Perl Documentation section, and it's literally about Bio::SeqFeature::SimilarityPair — a sequence feature that's built out of the similarity between two sequences. let's get into it 🦋

✨ NAME ✨

Bio::SeqFeature::SimilarityPair — a Sequence feature based on the similarity of two sequences. 🫶

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✨ SYNOPSIS ✨

like, here's the whole vibe in code form:

$sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);

$sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query
$sim = $sim_pair->hit();   # dto - the hit.

# some properties for the similarity pair
$expect = $sim_pair->significance();
$score = $sim_pair->score();
$bitscore = $sim_pair->bits();

# this will not write the description for the sequence (only its name)
print $sim_pair->query()->gff_string(), "\n";

no cap, that comment about gff_string() is doing important work — it only spits out the sequence's name, not the description. don't @ me, that's just what it says 💅

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✨ DESCRIPTION ✨

So this is a lightweight similarity search result, and the whole bit is that it's a pair of Similarity features. 🎀

It inherits off Bio::SeqFeature::FeaturePair, which means it implements Bio::SeqFeatureI (iconic, honestly). Meanwhile the two features of the pair are descendants of Bio::SeqFeature::Generic, and the whole point is better support for representing similarity search results in a cleaner way. ✨

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✨ FEEDBACK ✨

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. So like, 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. Bestie, there are so many experienced and reponsive experts who will be able look at the problem and quickly address it. If at all possible, please include a thorough description of the problem with code and data examples. the more detail the better, iykyk 💜

🐛 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 - Hilmar Lapp ✨

Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com 👑

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✨ APPENDIX ✨

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. 🌸

🌟 new

Title   : new
Usage   : my $similarityPair = Bio::SeqFeature::SimilarityPair->new
                                (-hit   => $hit,
                                 -query => $query,
                                 -source => 'blastp');
Function: Initializes a new SimilarityPair object
Returns : Bio::SeqFeature::SimilarityPair
Args    : -query => The query in a Feature pair
          -hit   => (formerly '-subject') the subject/hit in a Feature pair

okay so this one spins up a brand new SimilarityPair object. note that -hit used to be called -subject — glow-up era 💅

🌟 query

Title   : query
Usage   : $query_feature = $obj->query();
          $obj->query($query_feature);
Function: The query object for this similarity pair
Returns : Bio::SeqFeature::Similarity
Args    : [optional] Bio::SeqFeature::Similarity

See Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair. 🦋

🌟 subject

Title   : subject
Usage   : $sbjct_feature = $obj->subject();
          $obj->subject($sbjct_feature);
Function: Get/Set Subject for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args    : [optional] Bio::SeqFeature::Similarity

🌟 hit

Title   : hit
Usage   : $sbjct_feature = $obj->hit();
          $obj->hit($sbjct_feature);
Function: Get/Set Hit for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args    : [optional] Bio::SeqFeature::Similarity

🌟 source_tag

Title   : source_tag
Usage   : $source = $obj->source_tag(); # i.e., program
          $obj->source_tag($evalue);
Function: Gets the source tag (program name typically) for a feature
Returns : string
Args    : [optional] string

🌟 significance

Title   : significance
Usage   : $evalue = $obj->significance();
          $obj->significance($evalue);
Function:
Returns :
Args    :

🌟 score

Title   : score
Usage   : $score = $obj->score();
          $obj->score($value);
Function:
Returns :
Args    :

🌟 bits

Title   : bits
Usage   : $bits = $obj->bits();
          $obj->bits($value);
Function:
Returns :
Args    :

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and that's the whole page, bestie!! 🎀 this one's running on perl v5.32.1, dated 2021-08-15, and it's filed under Bio::S...ityPair(3pm). slay, go read some sequence features 💖✨👑