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

🎀 NAME 🎀

Bio::Align::ProteinStatistics — bestie, this is the module that crunches protein alignment statistics, and it's mostly about distances. That's the whole vibe. ✨

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🦋 SYNOPSIS 🦋

okay so here's how you actually use it, copy-paste core:

use Bio::Align::ProteinStatistics;
use Bio::AlignIO;
my $in = Bio::AlignIO->new(-format => 'fasta',
                          -file   => 'pep-104.fasaln');
my $aln = $in->next_aln;

my $pepstats = Bio::Align::ProteinStatistics->new();
$kimura = $protstats->distance(-align => $aln,
                               -method => 'Kimura');
print $kimura->print_matrix;

(yes, that's $pepstats up top and $protstats down below — that's literally how it's written, not me being messy 💀)

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💖 DESCRIPTION 💖

This object is your little machine for generating all kinds of statistics from a protein alignment. And the main character of that whole operation? pairwise protein distances. That's where it shines. periodt. 👑

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📚 REFERENCES 📚

• D_Kimura — Kimura, M. 1983. The Neutral Theory of Molecular Evolution. CUP, Cambridge.

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is, like, an integral part of the evolution of this and every other Bioperl module — fr fr. Send your comments and suggestions preferably to the Bioperl mailing list. 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. The reason is lowkey genius: so many experienced and responsive 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 of 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 - Jason Stajich 👑

Email jason-at-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 _ — that underscore is your little signal, iykyk. 🧚

🌟 new

Title   : new
Usage   : my $obj = Bio::Align::ProteinStatistics->new();
Function: Builds a new Bio::Align::ProteinStatistics object
Returns : an instance of Bio::Align::ProteinStatistics
Args    :

🌟 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 : L<Bio::Matrix::PhylipDist> object
Args    : -align  => Bio::Align::AlignI object
          -method => String specifying specific distance method
                     (implementing class may assume a default)

🌟 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

💅 D - distance methods 💅

🔥 D_Kimura

Title   : D_Kimura
Usage   : my $matrix = $pepstats->D_Kimura($aln);
Function: Calculate Kimura protein distance (Kimura 1983) which
          approximates PAM distance
          D = -ln ( 1 - p - 0.2 * p^2 )
Returns : L<Bio::Matrix::PhylipDist>
Args    : L<Bio::Align::AlignI>

🍓 Data Methods 🍓

🌈 pairwise_stats

Title   : pairwise_stats
Usage   : $obj->pairwise_stats($newval)
Function:
Returns : value of pairwise_stats
Args    : newvalue (optional)

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reminder bestie: every option, value, default and return type up there is exactly as written in the source. Don't freestyle them. 💖

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mwah, that's the whole page!! 💖 this lil doc shipped as part of perl v5.32.1, dated 2021-08-15, under the title Bio::A...tistics(3pm) — go forth and calculate those distances, you gorgeous genius. 🦋✨🎀