Linux Certif

Toute la documentation sur la certification Linux LPI

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

•

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 <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.