TFBS::...RANSFAC(3pm)

✨ NAME ✨

okay bestie, gather round 💖 — TFBS::DB::LocalTRANSFAC is the interface to a local transfac database position frequency matrices setup, straight out of the matrix.dat file. That's the whole vibe. 📁

This page lives in the User Contributed Perl Documentation, and yeah, the manual page name is a little eaten by the dots (TFBS::...RANSFAC), but we know who she is. 💅

-------------------------------- NOTICE ---------------------------------- The TRANSFAC database is free for non-commercial use. For commercial use the TRANSFAC databases and programs have to be licensed. Please read the DISCLAIMER at http://transfac.gbf.de/TRANSFAC/disclaimer.htm. -------------------------------------------------------------------------

real talk, that notice is not a joke — free for non-commercial, and if you're doing commercial stuff you have to license the TRANSFAC databases and programs. Go read the DISCLAIMER, fr fr. 🙈

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🌸 SYNOPSIS 🌸

• creating a database object by connecting to TRANSFAC data

my $db = TFBS::DB::LocalTRANSFAC->connect(-localdir => '/home/someusr');

localdir is the location of the matrix.dat TRANSFAC datafile 🗂️

• retrieving a TFBS::Matrix::* object from the database

# retrieving a PFM by ID
my $pfm = $db->get_Matrix_by_ID('V$CEBPA_01','PFM');

#retrieving a PWM by TRANSFAC accession number
my $pwm = $db->get_Matrix_by_acc('M00116', 'PWM');

See how she did both?? One by ID, one by accession number, and neither of them is even trying. 👑

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💜 DESCRIPTION 💜

TFBS::DB::LocalTRANSFAC is a read only database interface — so like, look but don't touch, bestie — that fetches TRANSFAC matrix data from a local TRANSFAC install (matrix.dat). 🧚

🎀 connect

• Title — connect
• Usage — my $db = TFBS::DB::TRANSFAC->connect(%args);
• Function — Creates a TRANSFAC database connection object, which can be used to retrieve matrices from a locally installed TRANSFAC database
• Returns — a TFBS::DB::TRANSFAC object
• Args —

-localdir    # REQUIRED: the directory of the matrix.dat TRANSFAC
             # datafile.  matrix.dat must have read access.
-accept_conditions # OPTIONAL: by setting this to a true
                   # value, you confirm that you
                   # have read and accepted the terms
                   # of use of TRANSFAC at
                   # http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
                   # this also suppresses the annoying
                   # message that is printed to STDERR
                   # upon invoking the method

So quick rundown on those args 💖

• -localdir — REQUIRED, no cap. It's the directory of the matrix.dat TRANSFAC datafile. And heads up: matrix.dat must have read access, or she cannot serve. 😭
• -accept_conditions — OPTIONAL. Set it to a true value and boom, you're confirming that you have read and accepted the terms of use of TRANSFAC at http://transfac.gbf.de/TRANSFAC/disclaimer.htm. Bonus: it also suppresses the annoying message that gets printed to STDERR when the method is invoked. iconic little two-for-one. ✨

🦋 get_Matrix_by_acc

• Title — get_Matrix_by_acc
• Usage — my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');
• Function — fetches matrix data under the given TRANSFAC accession number from database and returns a TFBS::Matrix::* object
• Returns — a TFBS::Matrix::* object; the exact type of the object depending on the second argument (allowed values are 'PFM', 'ICM', and 'PWM'); returns undef if matrix with the given ID is not found
• Args — (Matrix_ID, Matrix_type)
  • Matrix_ID is a string; Matrix_type is one of the following: 'PFM' (raw position frequency matrix), 'ICM' (information content matrix) or 'PWM' (position weight matrix)
  • If Matrix_type is omitted, a PFM is retrieved by default.

ngl the "returns undef if matrix with the given ID is not found" bit is the part you're gonna want to actually check for, bestie — she will not yell at you, she'll just hand you undef and let you figure it out. 💀

🌈 get_Matrix_by_ID

• Title — get_Matrix_by_ID
• Usage — my $pfm = $db->get_Matrix_by_ID('V$CREB_01', 'PFM');
• Function — fetches matrix data under the given TRANSFAC ID from the database and returns a TFBS::Matrix::* object
• Returns — a TFBS::Matrix::* object; the exact type of the object depending on the second argument (allowed values are 'PFM', 'ICM', and 'PWM'); returns undef if matrix with the given ID is not found
• Args — (Matrix_ID, Matrix_type)
  • Matrix_ID is a string; Matrix_type is one of the following: 'PFM' (raw position frequency matrix), 'ICM' (information content matrix) or 'PWM' (position weight matrix)
  • If Matrix_type is omitted, a PFM is retrieved by default.

Same energy as get_Matrix_by_acc, just keyed on the TRANSFAC ID instead of the accession number. Two doors, same room, both slay. 🚪✨

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and that's the page!! you ate 🫶 this whole thing came to you from perl v5.42.3, dated 2026-08-21 — so go forth, connect, and pull those matrices. periodt. 💅🎀