TFBS::DB::JASPAR5(3) interface to MySQL relational database of pattern matrices. Currently status: experimental.

SYNOPSIS

  • creating a database object by connecting to the existing JASPAR5-type database


    my $db = TFBS::DB::JASPAR5->connect("dbi:mysql:JASPAR5: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:
         @namelist = ('p50', 'p53', 'HNF-1'. 'GATA-1', 'GATA-2', 'GATA-3');
        my $matrixset = $db->get_MatrixSet(-names => \@namelist,
                                           -matrixtype => "ICM");
    
  • creating a new JASPAR5-type database named MYJASPAR5:

        my $db = TFBS::DB::JASPAR4->create("dbi:mysql:MYJASPAR5: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::JASPAR5 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 JASPAR2 and JASPAR4 interface, while the underlying data model is different

JASPAR5 DATA MODEL

JASPAR5 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, and custom, tags.

Here goes a moore thorough description on tables and IDs

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

For the developers and the curious, here is the JASPAR5 data model:

MISSING TEXT HEER ON HOW IT WORKS

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

connect

 Title   : connect
 Usage   : my $db =
            TFBS::DB::JASPAR5->connect("dbi:mysql:DATABASENAME:HOSTNAME",
                                        "USERNAME",
                                        "PASSWORD");
 Function: connects to the existing JASPAR5-type database and
           returns a database object that interfaces the database
 Returns : a TFBS::DB::JASPAR5 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; [email protected] 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
    # might have to give version and collection here
 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 id is a string which refers to the stable 
           JASPAR ID (usually something like "MA0001") with 
           or without version numbers. "MA0001" will give the 
           latest version on MA0001, while "MA0001.2" will give
           the second version, if existing. Warnings will be 
           given for non-existing matrices.

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 JASPAR5 data model, name is
           not necessarily a unique identifier. Also, names change 
           over time. 
           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.
           Some matrices have multiple versions. The function will 
           return the latest version. For specific versions, use 
           get_Matrix_by_ID($ID.$version)

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, and also some utility functions
           Note that this is different from JASPAR2 and to some extent JASPAR4. As any tag is supported for
           database storage, any tag can be used for information retrieval.
           Additionally, arguments as 'name','class','collection' can be used (even though
           they are not tags.
           Per default, only the last version of the matrix is given. The only way to get older matrices out of this 
           to use an array of IDs with actual versions like MA0001.1, or set the argyment -all_versions=>1, in which  case you get all versions for each stable ID
                                                                               
                                                                               
           
          Examples include:
 Fundamental matrix features
        -all # gives absolutely all matrix entry, regardless of versin and collection. Only useful for backup situations and sanity checks. Takes precedence over everything else
                
        -ID        # a reference to an array of stable IDs (strings), with or without version, as above. tyically something like "MA0001.2" . Takes precedence over everything salve -all               
 -name      # a reference to an array of
                       #  transcription factor names (string). Will only take latest version. NOT a preferred way to access since names change over time
           -collection # a string corresponding to a JASPAR collection. Per default CORE      
           -all_versions # gives all matrix versions that fit with rest of criteria, including obsolete ones.Is off per default. 
                         # Typical usage is in combiation with a stable IDs withou versions to get all versinos of a particular matrix          
          Typical tag queries:
        These can be either a string or a reference to an array of strings. If it is an arrau it will be interpreted as as an "or"s statement                                                                  
           -class    # a reference to an array of
                       #  structural class names (strings)
           -species    # a reference to an array of
                       #   NCBI Taxonomy IDs (integers)
           -taxgroup  # a reference to an array of
                       #  higher taxonomic categories (string)

Computed features of the matrices      
         -min_ic # float, minimum total information content
                 # of the matrix.
        -matrixtype #string describing type of matrix to retrieve. If left out, the format

                        will revert to the database format, which 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_CLUSTEROR'FORKHEAD') AND (the species they are derived
 from is 'Homo sapiens'OR 'Mus musculus').

As above, unless IDs with version numbers are used, only one matrix per stable ID wil be returned: the matrix with the highest version number

The -min_ic filter is applied after the query in the sense that the matrices profiles with total information 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('M00045.1');
 Function: Deletes the matrix having the given ID from the database
 Returns : 0 on success; [email protected] contents on failure
           (this is too C-ike and may change in future versions)
 Args    : (ID)
           A string. Has to be a matrix ID with version suffix in JASPAR5.
 Comment : Yeah, yeah, 'delete_Matrix_having_ID' is a stupid name
           for a method, but at least it should be obviuos what it does.