Provided by: libtfbs-perl_0.5.svn.20100421-1build1_amd64 bug

NAME

       TFBS::DB::JASPAR2 - 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::JASPAR2->connect("dbi:mysql:JASPAR2: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 JASPAR2-type database named MYJASPAR2:

               my $db = TFBS::DB::JASPAR2->create("dbi:mysql:MYJASPAR2: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::JASPAR2 is a read/write database interface module that retrieves and stores
       TFBS::Matrix::* and TFBS::MatrixSet objects in a relational database.

JASPAR2 DATA MODEL

       JASPAR2 is working name for a relational database model used for storing transcriptional
       factor pattern matrices in a MySQL database.  It was initially designed 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 optional tags.

       Due to its data model, which precedeed the design of the module, TFBS::DB::JASPAR2 cannot
       store arbitrary tags for a matrix.

       The supported tags are
           'acc'      # (accession number;             # originally for transcription factor
       protein seq)
           'seqdb'    # sequence database where 'acc' comes from
           'medline'  # PubMed ID
           'species'  # Species name
           'sysgroup'
           'total_ic' # total information content - redundant, present
                      # for historical "medline" => ($self->_get_medline($ID) or  ""),
       "species" => ($self->_get_species($ID) or ""),                     "sysgroup"=>
       ($self->_get_sysgroup($ID) or ""),                     "type"    => ($self->_get_type($ID)
       or ""),                     "seqdb"   => ($self->_get_seqdb($ID) or ""),
       "acc"     => ($self->_get_acc($ID) or ""),                     "total_ic"=

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

       For the developers and the curious, here is the JASPAR2 data model:

              CREATE TABLE matrix_data (
                ID varchar(16) DEFAULT '' NOT NULL,
                pos_ID varchar(24) DEFAULT '' NOT NULL,
                base enum('A','C','G','T'),
                position tinyint(3) unsigned,
                raw int(3) unsigned,
                info float(7,5) unsigned, -- calculated
                pwm float(7,5) unsigned,  -- calculated
                normalized float(7,5) unsigned,
                PRIMARY KEY (pos_ID),
                KEY id_index (ID)
              );

              CREATE TABLE matrix_info (
                ID varchar(16) DEFAULT '' NOT NULL,
                name varchar(15) DEFAULT '' NOT NULL,
                type varchar(8) DEFAULT '' NOT NULL,
                class varchar(20),
                phylum varchar (32),          -- maps to 'sysgroup' tag
                litt varchar(40),             -- not used by this module
                medline int(12),
                information varchar(20),      -- not used by this module
                iterations varchar(6),
                width int(2),                 -- calculated
                consensus varchar(25),        -- calculated
                IC float(6,4),                -- maps to 'total_ic' tag
                sites int(3) unsigned,        -- not used by this module
                PRIMARY KEY (ID)
              )

              CREATE TABLE matrix_seqs (
                ID varchar(16) DEFAULT '' NOT NULL,
                internal varchar(8) DEFAULT '' NOT NULL,
                seq_db varchar(15) NOT NULL,
                seq varchar(10) NOT NULL,
                PRIMARY KEY (ID, seq_db, seq)
              )

              CREATE TABLE matrix_species (
                ID varchar(16) DEFAULT '' NOT NULL,
                internal varchar(8) DEFAULT '' NOT NULL,
                species varchar(24) NOT NULL,
                PRIMARY KEY (ID, species)
              )

       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, simply because for historical reasons some
       table column names are confusing at best. 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::JASPAR2->connect("dbi:mysql:DATABASENAME:HOSTNAME",
                                               "USERNAME",
                                               "PASSWORD");
        Function: connects to the existing JASPAR2-type database and
                  returns a database object that interfaces the database
        Returns : a TFBS::DB::JASPAR2 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 acces permissions for
                  the database server.

   create
        Title   : create
        Usage   : my $newdb =
                   TFBS::DB::JASPAR2->create("dbi:mysql:NEWDATABASENAME:HOSTNAME",
                                             "USERNAME",
                                             "PASSWORD");
        Function: connects to the database server, creates a new JASPAR2-type database and returns a database
                  object that interfaces the database
        Returns : a TFBS::DB::JASPAR2 object
        Args    : a standard database connection triplet
                   ("dbi:mysql:NEWDATABASENAME:HOSTNAME",  "USERNAME", "PASSWORD")
                  In place of NEWDATABASENAME, HOSTNAME, USERNAME and
                  PASSWORD use the actual values. PASSWORD and USERNAME
                  might be optional, depending on the users 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

   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.

   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:
                  -IDs        # a reference to an array of IDs (strings)
                  -names      # a reference to an array of
                              #  transcription factor names (string)
                  -classes    # a reference to an array of
                              #  structural class names (strings)
                  -species    # a reference to an array of
                              #   Latin species names (strings)
                  -sysgroups  # a reference to an array of
                              #  higher taxonomic categories (strings)

                  -matrixtype # a string, 'PFM', 'ICM' or 'PWM'
                  -min_ic     # float, minimum total information content
                              #   of the matrix

       The five 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->(-classes => ['TRP_CLUSTER', 'FORKHEAD'],
                                 -species => ['Homo sapiens', 'Mus musculus'],
                                 -matrixtype => 'PWM');

       gives a set of PWMs 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.

   store_Matrix
        Title   : store_Matrix
        Usage   : $db->store_Matrix($pfm);
        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 object
        Comment : this is an experimental method that is not 100% bulletproof;
                  use at your own risk

   store_MatrixSet
        Title   : store_MatrixSet
        Usage   : $db->store_Matrix($matrixset);
        Function: Stores the TFBS::DB::PFM object that are part of a
                  TFBS::MatrixSet object into the database
        Returns : 0 on success; $@ contents on failure
                  (this is too C-like and may change in future versions)
        Args    : (MatrixSet_object)
                  A TFBS::MatrixSet object
        Comment : THIS METHOD IS NOT YET IMPLEMENTED

   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.