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.\" ========================================================================
.\"
.IX Title "TFBS::DB::FlatFileDir 3pm"
.TH TFBS::DB::FlatFileDir 3pm "2010-04-20" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
TFBS::DB::FlatFileDir \- interface to a database of pattern matrices
stored as a collection of flat files in a dedicated directory
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.IP "\(bu" 4
creating a database object by connecting to the existing directory
.Sp
.Vb 1
\&    my $db = TFBS::DB::FlatFileDir\->connect("/home/boris/MatrixDir");
.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(\*(AqM00079\*(Aq,\*(AqPFM\*(Aq);
\& 
\&    #retrieving a PWM by name
\&    my $pwm = $db\->get_Matrix_by_name(\*(AqNF\-kappaB\*(Aq, \*(AqPWM\*(Aq);
.Ve
.IP "\(bu" 4
retrieving a set of matrices as a TFBS::MatrixSet object according to various criteria
.Sp
.Vb 4
\&    # retrieving a set of PWMs from a list of IDs:
\&    my @IDlist = (\*(AqM0019\*(Aq, \*(AqM0045\*(Aq, \*(AqM0073\*(Aq, \*(AqM0101\*(Aq);
\&    my $matrixset = $db\->get_MatrixSet(\-IDs => \e@IDlist,
\&                                       \-matrixtype => "PWM");
\& 
\&    # retrieving a set of ICMs from a list of names:
\&    my @namelist = (\*(Aqp50\*(Aq, \*(Aqp53\*(Aq, \*(AqHNF\-1\*(Aq. \*(AqGATA\-1\*(Aq, \*(AqGATA\-2\*(Aq, \*(AqGATA\-3\*(Aq);
\&    my $matrixset = $db\->get_MatrixSet(\-names => \e@namelist,
\&                                       \-matrixtype => "ICM");
\& 
\&    # retrieving a set of all PFMs in the database
\&    my $matrixset = $db\->get_MatrixSet(\-matrixtype => "PFM");
.Ve
.IP "\(bu" 4
creating a new FlatFileDir database in a new directory:
.Sp
.Vb 1
\&    my $db = TFBS::DB::JASPAR2\->create("/home/boris/NewMatrixDir");
.Ve
.IP "\(bu" 4
storing a matrix in the database:
.Sp
.Vb 2
\&    #let $pfm is a TFBS::Matrix::PFM object
\&    $db\->store_Matrix($pfm);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
TFBS::DB::FlatFileDir is a read/write database interface module that
retrieves and stores TFBS::Matrix::* and TFBS::MatrixSet
objects in a set of flat files in a dedicated directory. It has a
very simple structure and can be easily set up manually if desired.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- Boris Lenhard"
.IX Header "AUTHOR - Boris Lenhard"
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
.SS "new"
.IX Subsection "new"
.Vb 8
\& Title   : new
\& Usage   : my $db = TFBS::DB::FlatFileDir\->new(%args);
\& Function: the formal constructor for the TFBS::DB::FlatFileDir object;
\&           most users will not use it \- they will use specialized
\&           I<connect> or I<create> constructors to create a
\&           database object
\& Returns : a TFBS::DB::FlatFileDir object
\& Args    : \-dir       # the directory containing flat files
.Ve
.SS "connect"
.IX Subsection "connect"
.Vb 8
\& Title   : connect
\& Usage   : my $db = TFBS::DB::FlatFileDir\->connect($directory);
\& Function: Creates a database object that retrieves TFBS::Matrix::*
\&           object data from or stores it in an existing directory
\& Returns : a TFBS::DB::FlatFileDir object
\& Args    : ($directory)
\&            The name of the directory (possibly with fully qualified
\&            path).
.Ve
.SS "create"
.IX Subsection "create"
.Vb 9
\& Title   : create
\& Usage   : my $newdb = TFBS::DB::FlatFileDir\->create($new_directory);
\& Function: connects to the database server, creates a new directory,
\&           sets up a FlatFileDir database and returns a database
\&           object that interfaces the database
\& Returns : a TFBS::DB::FlatFileDir object
\& Args    : ($new_directory)
\&            The name of the directory to create
\&            (possibly with fully qualified path).
.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(\*(AqM00034\*(Aq, \*(AqPFM\*(Aq);
\& Function: fetches matrix data under the given 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 PWM is retrieved by default.
.Ve
.SS "get_Matrix_by_name"
.IX Subsection "get_Matrix_by_name"
.Vb 10
\& Title   : get_Matrix_by_name
\& Usage   : my $pfm = $db\->get_Matrix_by_name(\*(AqHNF\-1\*(Aq, \*(AqPWM\*(Aq);
\& Function: fetches matrix data under the given name 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)
\& Args    : (Matrix_name, Matrix_type)
\&           Matrix_name 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 PWM is retrieved by default.
\& Warning : According to the current JASPAR2 data model, name is
\&           not necessarily a unique identifier. In the case where
\&           there are several matrices with the same name in the
\&           database, the function fetches the first one and prints
\&           a warning on STDERR. You have been warned.
.Ve
.SS "store_Matrix"
.IX Subsection "store_Matrix"
.Vb 6
\& Title   : store_Matrix
\& Usage   : $db\->store_Matrix($matrixobj);
\& Function: Stores the contents of a TFBS::Matrix::DB object in the database
\& Returns : 0 on success; $@ contents on failure
\&           (this is too C\-like and may change in future versions)
\& Args    : ($matrixobj) # a TFBS::Matrix::* object
.Ve
.SS "delete_Matrix_having_ID"
.IX Subsection "delete_Matrix_having_ID"
.Vb 9
\& Title   : delete_Matrix_having_ID
\& Usage   : $db\->delete_Matrix_with_ID(\*(AqM00045\*(Aq);
\& Function: Deletes the matrix having the given ID from the database
\& Returns : 0 on success; $@ contents on failure
\&           (this is too C\-like and may change in future versions)
\& Args    : (ID)
\&           A string
\& Comment : Yeah, yeah, \*(Aqdelete_Matrix_having_ID\*(Aq is a stupid name
\&           for a method, but at least it should be obviuos what it does.
.Ve