TFBS::...ANSFAC(3pm)

💖 TFBS::DB::TRANSFAC — the manual page, but make it make sense 💖

okay bestie, so this is the perl doc for TFBS::DB::TRANSFAC (shipped under the manual name TFBS::...ANSFAC(3pm), part of the User Contributed Perl Documentation situation). It's giving "I need transcription factor binding site matrices and I need them from the internet." Sit down, get a strawberry drink, we're doing this 🍓

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🚨 NOTICE 🚨

-------------------------------- 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. -------------------------------------------------------------------------

fr fr, read that twice. Non-commercial = free, commercial = you gotta get a license, no cap. The DISCLAIMER lives at http://transfac.gbf.de/TRANSFAC/disclaimer.htm 💅

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✨ NAME ✨

TFBS::DB::TRANSFAC — an interface to the database of TRANSFAC public position frequency matrices over at TESS (http://www.cbil.upenn.edu/tess). It's the little doorway between your perl script and a whole bunch of matrices. iconic behavior 💖

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🦋 SYNOPSIS 🦋

• making a database object by connecting to TRANSFAC data — the whole "hi hello let me in" moment:

my $db = TFBS::DB::TRANSFAC->connect();

• pulling a TFBS::Matrix::* object out of the database — this is the part where you actually get your little matrix:

# 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');

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🌸 DESCRIPTION 🌸

TFBS::DB::TRANSFAC is a read only database interface — like, you're not writing anything back, you're just grabbing. It fetches TRANSFAC matrix data from the TESS web interface (http://www.cbil.upen.edu/TESS) and hands you back TFBS::Matrix::* objects. Simple. Elegant. Slay.

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🎀 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 public TRANSFAC databases via the web
• Returns: a TFBS::DB::TRANSFAC object
• Args:
  • -proxy — # OPTIONAL: a http proxy server name, usually required for accessing TRANSFAC from behind a firewall
  • -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 yeah, the proxy one is for when you're sitting behind a firewall and the vibe check fails without it 🔥 and -accept_conditions is basically you signing the little permission slip and muting the annoying STDERR message at the same time. two birds, one true value 💅

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🧚 new

• Title: connect
• Usage: my $db = TFBS::DB::TRANSFAC->connect(%args);
• Function: Here, new is just a synonim for connect (to make the interface consistent with other bioperl read-obly Bio::DB::* objects)
• Returns: a TFBS::DB::TRANSFAC object
• Args:
  • -accept_conditions — # see explanation at new

okay yes the Title and Usage say connect even though you're reading about new — that's not me being chaotic, that's literally what the page says, I'm just the messenger 🙈 and yeah, -accept_conditions here means "go look at the explanation at new", which is... this one. we love a circular moment.

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🌈 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.

so you hand it an ID and you tell it what flavor you want, and it gives you the goods. if the ID isn't a thing, you get undef — which is code for "girl, that matrix does not exist" 😭 default flavor is 'PFM', no need to spell it out if that's what you're after 👑

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💜 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.

literally the same energy as above but you're looking it up by TRANSFAC accession number instead of ID. same return rules: TFBS::Matrix::* object back, type depends on the second arg ('PFM', 'ICM', 'PWM'), undef if it's not found. and again — omit the type and you're getting a PFM, periodt ✨

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also just like, a general reminder bestie: this whole thing is read only. you fetch, you don't push. 💖

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and that's the page!! no cap, every flag, every arg, every default, every URL — it's all here 🫶 this was perl v5.42.3, dated 2026-08-21, manual name TFBS::...ANSFAC(3pm). go get your matrices, you're gonna eat 💅🌸