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NAME

       TFBS::DB::JASPAR4 - interface to MySQL relational database of pattern
       matrices

SYNOPSIS

       ·   creating a database object by connecting to the existing
           JASPAR2-type database

               my $db = TFBS::DB::JASPAR4->connect("dbi:mysql:JASPAR4:myhost",
                                                   "myusername",
                                                   "mypassword");

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

               # retrieving a PFM by ID
               my $pfm = $db->get_Matrix_by_ID('M0079','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
               # derived from human genes:
               my $matrixset = $db->get_MatrixSet(-species => ['Homo sapiens'],
                                                  -matrixtype => "PFM");

       ·   creating a new JASPAR4-type database named MYJASPAR4:

               my $db = TFBS::DB::JASPAR4->create("dbi:mysql:MYJASPAR4:myhost",
                                                  "myusername",
                                                  "mypassword");

       ·   storing a matrix in the database (currently only PFMs):

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

DESCRIPTION

       TFBS::DB::JASPAR4 is a read/write database interface module that
       retrieves and stores TFBS::Matrix::* and TFBS::MatrixSet objects in a
       relational database. The interface is nearly identical to the
       JASPAR2interface, while the underlying data model is different

JASPAR2 DATA MODEL

       JASPAR4 is working name for a relational database model used for
       storing transcriptional factor pattern matrices in a MySQL database.
       It was initially designed (JASPAR2) to store matrices for the JASPAR
       database of high quality eukaryotic transcription factor specificity
       profiles by Albin Sandelin and Wyeth W. Wasserman. Besides the profile
       matrix itself, this data model stores profile ID (unique), name,
       structural class, basic taxonomic and bibliographic information as well
       as some additional opseqdbtional tags.

       Tags that are commonly used in the actual JASPAR database include
           'medline'  # PubMed ID
           'species'  # Species name
           'superclass' #Species supergroup, eg 'vertebrate', 'plant' etc
           'total_ic' # total information content - redundant, present
                      # for historical
           'type'    #experimental nethod
           'acc'    #accession number for TF protein sequence
           'seqdb'    #corresponding database name

       but any tag is storable and searchable.

       -----------------------  ADVANCED  ---------------------------------

       For the developers and the curious, here is the JASPAR4 data model:

       It is our best intention to hide the details of this data model, which
       we are using on a daily basis in our work, from most TFBS users.  Most
       users should only know the methods to store the data and which tags are
       supported.

       -------------------------------------------------------------------------

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   : DEPRECATED - for backward compatibility only
                  Use connect() or create() instead

   connect
        Title   : connect
        Usage   : my $db =
                   TFBS::DB::JASPAR4->connect("dbi:mysql:DATABASENAME:HOSTNAME",
                                               "USERNAME",
                                               "PASSWORD");
        Function: connects to the existing JASPAR4-type database and
                  returns a database object that interfaces the database
        Returns : a TFBS::DB::JASPAR4 object
        Args    : a standard database connection triplet
                  ("dbi:mysql:DATABASENAME:HOSTNAME",  "USERNAME", "PASSWORD")
                  In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
                  use the actual values. PASSWORD and USERNAME might be
                  optional, depending on the user's acces permissions for
                  the database server.

   dbh
        Title   : dbh
        Usage   : my $dbh = $db->dbh();
                  $dbh->do("UPDATE matrix_data SET name='ADD1' WHERE NAME='SREBP2'");
        Function: returns the DBI database handle of the MySQL database
                  interfaced by $db; THIS IS USED FOR WRITING NEW METHODS
                  FOR DIRECT RELATIONAL DATABASE MANIPULATION - if you
                  have write access AND do not know what you are doing,
                  you can severely  corrupt the data
                  For documentation about database handle methods, see L<DBI>
        Returns : the database (DBI) handle of the MySQL JASPAR2-type
                  relational database associated with the TFBS::DB::JASPAR2
                  object
        Args    : none

   store_Matrix
        Title   : store_Matrix
        Usage   : $db->store_Matrix($matrixobject);
        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    : (PFM_object)
                  A TFBS::Matrix::PFM, FBS::Matrix::PWM or FBS::Matrix::ICM object.
                  PFM object are recommended to use, as they are eaily converted to
                  other formats
        Comment : this is an experimental method that is not 100% bulletproof;
                  use at your own risk

   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 what form the matrix is stored
                  in the database (PFM is default)
        Args    : (Matrix_ID)
                  Matrix_ID is a string;

   get_Matrix_by_name
        Title   : get_Matrix_by_name
        Usage   : my $pfm = $db->get_Matrix_by_name('HNF-1');
        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 what form the matrix object was stored in
                  the database (default PFM))
        Args    : (Matrix_name)

        Warning : According to the current JASPAR4 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've been warned.

   get_MatrixSet
        Title   : get_MatrixSet
        Usage   : my $matrixset = $db->get_MatrixSet(%args);
        Function: fetches matrix data under for all matrices in the database
                  matching criteria defined by the named arguments
                  and returns a TFBS::MatrixSet object
        Returns : a TFBS::MatrixSet object
        Args    : This method accepts named arguments, corresponding to arbitrary tags.
                  Note that this is different from JASPAR2. As any tag is supported for
                  database storage, any tag can be used for information retrieval.
                  Additionally, arguments as 'name' and 'class' can be used (even though
                  they are not tags.
                  As with get_Matrix methods, it is important to realize taht any matrix
                  format can be stored in the database: the TFBS::MatrixSet might therefore
                  consist of PFMs, ICMs and PWMS, depending on how matrices are stored,

                  Examples include
                  -ID        # a reference to an array of IDs (strings)
                  -name      # a reference to an array of
                              #  transcription factor names (string)
                  -class    # a reference to an array of
                              #  structural class names (strings)
                  -species    # a reference to an array of
                              #   Latin species names (strings)
                  -sysgroup  # a reference to an array of
                              #  higher taxonomic categories (strings)

                  -min_ic     # float, minimum total information content
                              #   of the matrix. IMPORTANT:if retrieved matrices are in PWM
                              format there is no way to measureinformation content.
               -matrixtype    #string describing type of matrix to retrieve. If left out, the format
                               will revert to the database format. Note that this option only works
                             if the database format is pfm

       The arguments that expect list references are used in database query
       formulation: elements within lists are combined with 'OR' operators,
       and the lists of different types with 'AND'. For example,

           my $matrixset = $db->(-class => ['TRP_CLUSTER', 'FORKHEAD'],
                                 -species => ['Homo sapiens', 'Mus musculus'],
                                 );

       gives a set of TFBS::Matrix::PFM objects (given that the matrix models
       are stored as such)
        whose (structural clas is 'TRP_CLUSTER' OR'FORKHEAD') AND (the species
       they are derived
        from is 'Homo sapiens'OR 'Mus musculus').

       The -min_ic filter is applied after the query in the sense that the
       matrices profiles with total infromation content less than specified
       are not included in the set.

   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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