TFBS::DB::FlatFileDir(3) interface to a database of pattern matrices

SYNOPSIS

  • creating a database object by connecting to the existing directory


    my $db = TFBS::DB::FlatFileDir->connect("/home/boris/MatrixDir");

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

        # retrieving a PFM by ID
        my $pfm = $db->get_Matrix_by_ID('M00079','PFM');
     
        #retrieving a PWM by name
        my $pwm = $db->get_Matrix_by_name('NF-kappaB', 'PWM');
    
  • retrieving a set of matrices as a TFBS::MatrixSet object according to various criteria

        # retrieving a set of PWMs from a list of IDs:
        my @IDlist = ('M0019', 'M0045', 'M0073', 'M0101');
        my $matrixset = $db->get_MatrixSet(-IDs => \@IDlist,
                                           -matrixtype => "PWM");
     
        # retrieving a set of ICMs from a list of names:
        my @namelist = ('p50', 'p53', 'HNF-1'. 'GATA-1', 'GATA-2', 'GATA-3');
        my $matrixset = $db->get_MatrixSet(-names => \@namelist,
                                           -matrixtype => "ICM");
     
        # retrieving a set of all PFMs in the database
        my $matrixset = $db->get_MatrixSet(-matrixtype => "PFM");
    
  • creating a new FlatFileDir database in a new directory:

        my $db = TFBS::DB::JASPAR2->create("/home/boris/NewMatrixDir");
    
  • storing a matrix in the database:

        #let $pfm is a TFBS::Matrix::PFM object
        $db->store_Matrix($pfm);
    

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.

FEEDBACK

Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

Boris Lenhard <[email protected]>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.

new

 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

connect

 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).

create

 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).

get_Matrix_by_ID

 Title   : get_Matrix_by_ID
 Usage   : my $pfm = $db->get_Matrix_by_ID('M00034', 'PFM');
 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 '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 PWM is retrieved by default.

get_Matrix_by_name

 Title   : get_Matrix_by_name
 Usage   : my $pfm = $db->get_Matrix_by_name('HNF-1', 'PWM');
 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
           'PFM', 'ICM', and 'PWM')
 Args    : (Matrix_name, Matrix_type)
           Matrix_name 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 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.

store_Matrix

 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; [email protected] contents on failure
           (this is too C-like and may change in future versions)
 Args    : ($matrixobj) # a TFBS::Matrix::* object

delete_Matrix_having_ID

 Title   : delete_Matrix_having_ID
 Usage   : $db->delete_Matrix_with_ID('M00045');
 Function: Deletes the matrix having the given ID from the database
 Returns : 0 on success; [email protected] contents on failure
           (this is too C-like and may change in future versions)
 Args    : (ID)
           A string
 Comment : Yeah, yeah, 'delete_Matrix_having_ID' is a stupid name
           for a method, but at least it should be obviuos what it does.