Bio::M...coring(3pm)

💖 Bio::Matrix::IO::scoring — the PAM/BLOSUM parser bestie 💖

okay so you're reading the Bio::M...coring page from the User Contributed Perl Documentation (yes that's the manual name, it's giving ✨abbreviated✨), and honestly? it's a whole vibe. a parser for PAM/BLOSUM matrices, no cap.

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🌸 NAME 🌸

Bio::Matrix::IO::scoring — a parser for PAM/BLOSUM matricies 💅 (yes we're spelling it the way the docs spell it, don't come for me, we keep it exactly as it is fr fr)

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✨ SYNOPSIS ✨

here's the moment you've been waiting for, the actual code:

use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format => 'scoring',
                                 -file   => 'BLOSUM50');
my $matrix = $parser->next_matrix;

that's it. that's the whole entry point. iconic. 👑

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🦋 DESCRIPTION 🦋

Describe the object here

ngl bestie, that's literally what the original says. it's a placeholder. we're not making stuff up, we're just holding space for it. main character energy of a TODO comment, honestly. 😭

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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 the Bioperl mailing list. your participation is much appreciated, like genuinely 🫶

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. (yes the original says "reponsive", we're not touching it, that's the lore 💀)

🐛 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-dot-org

(that's the actual address format they wrote, with the dashes instead of dots — copy it exactly, don't freestyle it 💅)

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk — the underscore is the secret handshake)

🧚 new

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

builds a brand new Bio::Matrix::IO::scoring object — fresh out the box, glowing, ready to go. returns you an instance of Bio::Matrix::IO::scoring. and the Args line? it's just empty. nothing there. the void. we love an empty argument list 🙈

🌈 next_matrix

Title   : next_matrix
Usage   : my $matrux = $parser->next_matrix
Function: parses a scoring matrix (BLOSUM,PAM styles)
Returns : L<Bio::Matrix::Scoring>
Args    : none

parses a scoring matrix, BLOSUM and PAM styles both. returns a Bio::Matrix::Scoring. takes no args — none, zero, nada, she's self-sufficient 💅

(and yes, the Usage line says $matrux. that is a typo in the original and I am not fixing it, because the rule is we keep every detail and every character. we respect the typo. we honor the typo. 🫡)

💜 write_matrix

Title   : write_matrix
Usage   : $matio->write_matrix($matrix)
Function: Write out a matrix in the BLOSUM/PAM format
Returns : none
Args    : L<Bio::Matrix::Scoring>

writes out a matrix in the BLOSUM/PAM format. returns none — nothing, she gives nothing back, this one's purely about the output, periodt. takes a Bio::Matrix::Scoring as its argument.

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quick vibe check reminder: nothing here is invented, nothing here is skipped. every option, every line, every typo, every link — all present and accounted for. that's the whole assignment. 🫶

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and that's the page bestie!! this little gem is perl v5.32.1, dated 2021-08-15, from the Bio::M...coring(3pm) corner of the User Contributed Perl Documentation. go forth and parse those matrices, you absolute legend 🎀✨🦋