TFBS::DB::FlatFileDir(3pm)

NAME

TFBS::DB::FlatFileDir - interface to a database of pattern matrices
stored as a collection of flat files in a dedicated directory

SYNOPSIS

o   creating a database object by connecting to the existing directory

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

o   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');

o   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");

o   creating a new FlatFileDir database in a new directory:

        my $db = TFBS::DB::JASPAR2->create("/home/boris/NewMatrixDir");

o   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 <Boris.Lenhard@cgb.ki.se>

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; $@ contents on failure
(this is too C-like and may change in future versions); Args : ($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; $@ 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.

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