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

✨ NAME ✨

Bio::SeqFeature::Similarity — a sequence feature based on similarity 💖

okay so basically, this is the manual page for Bio::S...ilarity(3pm) and we are gonna get into it 💅

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🌸 SYNOPSIS 🌸

# obtain a similarity feature somehow
print "significance: ", $sim_fea->significance(), "\n";
print "bit score: ", $sim_fea->bits(), "\n";
print "score: ", $sim_fea->score(), "\n";
print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n";

like, you get a similarity feature somehow (that's on you bestie, the getting is not our problem 💀) and then you can pull all the juicy numbers out of it ✨

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🦋 DESCRIPTION 🦋

So this module is basically a sequence feature based on similarity, which means it has support for measures that assess the similarity. that's the whole vibe 🫶

Everything else is inherited from Bio::SeqFeature::Generic — so anything you don't see here? it's living over there, being iconic in its own file 👑

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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 💖

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.

fr fr, go to the list first, not the maintainer's DMs — the experts are right there and they're ready to help 🙈

🐛 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 _ (iykyk, underscore = backstage, not main character energy 💅)

significance

• Title — significance
• Usage —

$evalue = $obj->significance();
$obj->significance($evalue);

• Function —
• Returns —
• Args —

bits

• Title — bits
• Usage —

$bits = $obj->bits();
$obj->bits($value);

• Function —
• Returns —
• Args —

frac_identical

• Title — frac_identical
• Usage —

$fracid = $obj->frac_identical();
$obj->frac_identical($value);

• Function —
• Returns —
• Args —

seqlength

• Title — seqlength
• Usage —

$len = $obj->seqlength();
$obj->seqlength($len);

• Function —
• Returns —
• Args —

seqdesc

• Title — seqdesc
• Usage —

$desc = $obj->seqdesc();
$obj->seqdesc($desc);

• Function — At present this method is a shorthand for $obj->annotation()->description().

heads up bestie: note that this is not stored in the tag system and hence will not be included in the return value of gff_string() 🚨 like, it's just not gonna show up there, no cap

• Returns —
• Args —

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and that's the whole page, babe 💜 this one's from perl v5.32.1, dated 2021-08-15, and yes the manual name really is Bio::S...ilarity(3pm) — they did that, and honestly? iconic 🌈✨ slay, go read your features 🎀🦋