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.IX Title "TFBS::DB::LocalTRANSFAC 3pm"
.TH TFBS::DB::LocalTRANSFAC 3pm 2024-03-13 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH NAME
TFBS::DB::LocalTRANSFAC \- interface to local transfac database
position frequency matrices (matrix.dat)
.PP
.Vb 5
\& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- 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.
\& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
.Ve
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.IP \(bu 4
creating a database object by connecting to TRANSFAC data
.Sp
.Vb 1
\&    my $db = TFBS::DB::LocalTRANSFAC\->connect(\-localdir => \*(Aq/home/someusr\*(Aq);
\&
\&    localdir is the location of the matrix.dat TRANSFAC datafile
.Ve
.IP \(bu 4
retrieving a TFBS::Matrix::* object from the database
.Sp
.Vb 2
\&    # retrieving a PFM by ID
\&    my $pfm = $db\->get_Matrix_by_ID(\*(AqV$CEBPA_01\*(Aq,\*(AqPFM\*(Aq);
\&
\&    #retrieving a PWM by TRANSFAC accession number
\&    my $pwm = $db\->get_Matrix_by_acc(\*(AqM00116\*(Aq, \*(AqPWM\*(Aq);
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
TFBS::DB::LocalTRANSFAC is a read only database interface that fetches
TRANSFAC matrix data from a local TRANSFAC install (matrix.dat)
.SS connect
.IX Subsection "connect"
.Vb 10
\& 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
.Ve
.SS get_Matrix_by_acc
.IX Subsection "get_Matrix_by_acc"
.Vb 10
\& Title   : get_Matrix_by_acc
\& Usage   : my $pfm = $db\->get_Matrix_by_acc(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq);
\& 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 \*(AqPFM\*(Aq, \*(AqICM\*(Aq, and \*(AqPWM\*(Aq); 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: \*(AqPFM\*(Aq (raw position frequency matrix),
\&           \*(AqICM\*(Aq (information content matrix) or \*(AqPWM\*(Aq (position
\&           weight matrix)
\&           If Matrix_type is omitted, a PFM is retrieved by default.
.Ve
.SS get_Matrix_by_ID
.IX Subsection "get_Matrix_by_ID"
.Vb 10
\& Title   : get_Matrix_by_ID
\& Usage   : my $pfm = $db\->get_Matrix_by_ID(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq);
\& 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 \*(AqPFM\*(Aq, \*(AqICM\*(Aq, and \*(AqPWM\*(Aq); 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: \*(AqPFM\*(Aq (raw position frequency matrix),
\&           \*(AqICM\*(Aq (information content matrix) or \*(AqPWM\*(Aq (position
\&           weight matrix)
\&           If Matrix_type is omitted, a PFM is retrieved by default.
.Ve