Bio::A...isticsI(3pm)

💖 Bio::Align::StatisticsI 💖

okay bestie, so this is a page from the User Contributed Perl Documentation, and the module is literally called Bio::Align::StatisticsI — it's the interface for crunching statistics on an alignment. Think distance matrices, methods, the whole vibe. It's giving ✨interface✨ (iykyk), which means the actual implementing classes do the heavy lifting and this page just tells you what they promise to do. 🫶

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🌸 NAME 🌸

Bio::Align::StatisticsI — Calculate some statistics for an alignment 💅

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🎀 SYNOPSIS 🎀

Give standard usage here 👑

Give standard usage here

no cap, that's literally what it says 🙈

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🦋 DESCRIPTION 🦋

Describe the interface here — yep, that's the whole thing. The docs are lowkey leaving it to your imagination, bestie. 💀

Describe the interface here

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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 the Bioperl mailing list. Your participation is much appreciated — like, genuinely, they mean it. 🥹

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. The way that many experienced and reponsive experts will be able look at the problem and quickly address it — iconic behavior honestly. 💅 Please include a thorough description of the problem with code and data examples if at all possible. (Yes, actual examples. Not just "it doesn't work." 😭)

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution — they're tracking them so you don't have to chase them around the group chat. 🕵️‍♀️ Bug reports can be submitted via the web:

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

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👑 AUTHOR - Jason Stajich 👑

Email jason@bioperl.org 💜

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🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — so if you see that underscore, mind your business, that's private. 🙈

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🍓 distance

• Title : distance
• Usage : my $distance_mat = $stats->distance(-align => $aln, -method => $method);
• Function: Calculates a distance matrix for all pairwise distances of sequences in an alignment. 🔥
• Returns : Array ref
• Args : -align => Bio::Align::AlignI object -method => String specifying specific distance method (implementing class may assume a default)

so basically: hand it an alignment and a method name, get back an array ref full of pairwise distances. slay. 💅

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🧚 available_distance_methods

• Title : available_distance_methods
• Usage : my @methods = $stats->available_distance_methods();
• Function: Enumerates the possible distance methods ✨
• Returns : Array of strings
• Args : none

no args, just vibes. ask it what methods exist, it tells you. main character energy. 👑

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💀 heads up bestie: this is an interface, so the implementing class may assume a default for -method — the page says so right there, don't come for me.

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and that's the whole page, babe! 🌸 This gorgeous little number is from perl v5.32.1, dated 2021-08-15, and it lives under the name Bio::A...isticsI(3pm). mwah 💋 go calculate some distances, you got this 🦋💖