TFBS::Matrix(3pm)

💖 NAME 💖

TFBS::Matrix — bestie, it's the base class for matrix patterns, and it's holding all the methods that literally every one of them shares 🫶

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✨ DESCRIPTION ✨

okay so TFBS::Matrix is a base class. What does that mean fr fr? It's the blueprint. It's giving main character energy but it does not get instantiated itself, okay? No solo debut for this one 💅

What it actually is: a universal constructor that its subclasses (TFBS::Matrix::*) call whenever they need to be born, plus a whole lil collection of matrix manipulation methods that don't care what type of matrix you handed them. Type-independent. Universal. Iconic.

Not meant to be instantiated itself. So don't try it, bestie, that's not her role 🌸

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📣 FEEDBACK 📣

Found a bug? Got thoughts? Comments? Not me gatekeeping feedback — please send bug reports and other comments to the author <3

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👑 AUTHOR - Boris Lenhard 👑

Boris Lenhard <Boris.Lenhard@cgb.ki.se>

Modified by Eivind Valen eivind.valen@gmail.com ✨

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🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Heads up: internal methods are preceded with an underscore — iykyk, those are the behind-the-scenes girlies 🙈

🧚 matrix

• Title: matrix
• Usage:

my $matrix = $pwm->matrix();
$pwm->matrix( [ [12, 3, 0, 0, 4, 0],
                [ 0, 0, 0,11, 7, 0],
                [ 0, 9,12, 0, 0, 0],
                [ 0, 0, 0, 1, 1,12]
              ]);

• Function: it's the get/set for the matrix data — grab it or set it, your call 💖
• Returns: a reference to a 2D array of integers (PFM) or floats (ICM, PWM)
• Args: none for a get; for a set you can pass a four line string, a reference to 2D array, or a 2D piddle

🦋 pdl_matrix

• Title: pdl_matrix
• Usage: my $pdl = $pwm->pdl_matrix();
• Function: access the PDL matrix used to store the actual matrix data, directly — no middleman, no filter 🫶
• Returns: a PDL object, aka a piddle</piddle>
• Args: none

🌈 revcom

• Title: revcom
• Usage: my $revcom_pfm = $pfm->revcom();
• Function: create a matrix pattern object which is the reverse complement of the current one — flip it and reverse it 🔥
• Returns: a TFBS::Matrix::* object of the same type as the one the method acted upon
• Args: none

💜 rawprint

• Title: rawprint
• Usage: my $rawstring = $pfm->rawprint);
• Function: convert matrix data to a simple, tab-separated format
• Returns: a four-line string of tab-separated integers or floats
• Args: none

🍓 prettyprint

• Title: prettyprint
• Usage: my $prettystring = $pfm->prettyprint();
• Function: convert matrix data to a human-readable string format — the glow-up version ✨
• Returns: a four-line string with nucleotides and aligned numbers
• Args: none

⭐ STAMPprint

• Title: STAMPprint
• Usage: my $STAMPstring = $pfm->STAMPprint();
• Function: convert the matrix to a STAMP readable format
• Returns: a string of the matrix in a TRANSFAC like format for STAMP
• Args: none

🎀 length

• Title: length
• Usage: my $pattern_length = $pfm->length;
• Function: gets the pattern length in nucleotides — that's the number of columns in the matrix, bestie
• Returns: an integer
• Args: none

💅 randomize_columns

• Title: randomize_columns
• Usage: $pfm->randomize_columns();
• Function: randomizes the columns of a matrix, in place — yes, it messes with the original, that's the whole point 🙈
• Returns: nothing
• Args: none

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okay bestie that's the whole page, no cap 💖 this was TFBS::Matrix(3pm) from the User Contributed Perl Documentation, sitting pretty at perl v5.42.3 and dated 2026-08-21. slay, go forth and matrix 🌸👑