File: TFBS%3A%3ADB%3A%3AJASPAR2.3pm

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.\" ========================================================================
.\"
.IX Title "TFBS::DB::JASPAR2 3"
.TH TFBS::DB::JASPAR2 3 "2005-01-04" "perl v5.12.4" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
TFBS::DB::JASPAR2 \- interface to MySQL relational database of pattern matrices
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.IP "\(bu" 4
creating a database object by connecting to the existing JASPAR2\-type database
.Sp
.Vb 3
\&    my $db = TFBS::DB::JASPAR2\->connect("dbi:mysql:JASPAR2:myhost",
\&                                        "myusername",
\&                                        "mypassword");
.Ve
.IP "\(bu" 4
retrieving a TFBS::Matrix::* object from the database
.Sp
.Vb 2
\&    # retrieving a PFM by ID
\&    my $pfm = $db\->get_Matrix_by_ID(\*(AqM0079\*(Aq,\*(AqPFM\*(Aq);
\& 
\&    #retrieving a PWM by name
\&    my $pwm = $db\->get_Matrix_by_name(\*(AqNF\-kappaB\*(Aq, \*(AqPWM\*(Aq);
.Ve
.IP "\(bu" 4
retrieving a set of matrices as a TFBS::MatrixSet object according to various criteria
.Sp
.Vb 4
\&    # retrieving a set of PWMs from a list of IDs:
\&    my @IDlist = (\*(AqM0019\*(Aq, \*(AqM0045\*(Aq, \*(AqM0073\*(Aq, \*(AqM0101\*(Aq);
\&    my $matrixset = $db\->get_MatrixSet(\-IDs => \e@IDlist,
\&                                       \-matrixtype => "PWM");
\& 
\&    # retrieving a set of ICMs from a list of names:
\&    my @namelist = (\*(Aqp50\*(Aq, \*(Aqp53\*(Aq, \*(AqHNF\-1\*(Aq. \*(AqGATA\-1\*(Aq, \*(AqGATA\-2\*(Aq, \*(AqGATA\-3\*(Aq);
\&    my $matrixset = $db\->get_MatrixSet(\-names => \e@namelist,
\&                                       \-matrixtype => "ICM");
\& 
\&    # retrieving a set of all PFMs in the database
\&    # derived from human genes:
\&    my $matrixset = $db\->get_MatrixSet(\-species => [\*(AqHomo sapiens\*(Aq],
\&                                       \-matrixtype => "PFM");
.Ve
.IP "\(bu" 4
creating a new JASPAR2\-type database named \s-1MYJASPAR2:\s0
.Sp
.Vb 3
\&    my $db = TFBS::DB::JASPAR2\->create("dbi:mysql:MYJASPAR2:myhost",
\&                                       "myusername",
\&                                       "mypassword");
.Ve
.IP "\(bu" 4
storing a matrix in the database (currently only PFMs):
.Sp
.Vb 2
\&    #let $pfm is a TFBS::Matrix::PFM object
\&    $db\->store_Matrix($pfm);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\s-1TFBS::DB::JASPAR2\s0 is a read/write database interface module that
retrieves and stores TFBS::Matrix::* and TFBS::MatrixSet
objects in a relational database.
.SH "JASPAR2 DATA MODEL"
.IX Header "JASPAR2 DATA MODEL"
\&\s-1JASPAR2\s0 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 \s-1JASPAR\s0 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 \s-1ID\s0 (unique), name, structural class,
basic taxonomic and bibliographic information
as well as some additional optional tags.
.PP
Due to its data model, which precedeed the design of the 
module, \s-1TFBS::DB::JASPAR2\s0 cannot store arbitrary tags for a matrix.
.PP
The supported tags are
    'acc'      # (accession number; 
	       # originally for transcription factor protein seq)
    'seqdb'    # sequence database where 'acc' comes from
    'medline'  # PubMed \s-1ID\s0
    'species'  # Species name
    'sysgroup'
    'total_ic' # total information content \- redundant, present 
               # for historical
\&\*(L"medline\*(R" => ($self\->_get_medline($ID) or  "\*(L"),
		          \*(R"species\*(L" => ($self\->_get_species($ID) or \*(R"\*(L"),
		          \*(R"sysgroup\*(L"=> ($self\->_get_sysgroup($ID) or \*(R"\*(L"),
		          \*(R"type\*(L"    => ($self\->_get_type($ID) or \*(R"\*(L"),
		          \*(R"seqdb\*(L"   => ($self\->_get_seqdb($ID) or \*(R"\*(L"),
		          \*(R"acc\*(L"     => ($self\->_get_acc($ID) or \*(R"\*(L"),
		          \*(R"total_ic"=
.PP
\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-  \s-1ADVANCED\s0  \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
.PP
For the developers and the curious, here is the \s-1JASPAR2\s0 data model:
.PP
.Vb 12
\&       CREATE TABLE matrix_data (
\&         ID varchar(16) DEFAULT \*(Aq\*(Aq NOT NULL,
\&         pos_ID varchar(24) DEFAULT \*(Aq\*(Aq NOT NULL,
\&         base enum(\*(AqA\*(Aq,\*(AqC\*(Aq,\*(AqG\*(Aq,\*(AqT\*(Aq),
\&         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 \*(Aq\*(Aq NOT NULL,
\&         name varchar(15) DEFAULT \*(Aq\*(Aq NOT NULL,
\&         type varchar(8) DEFAULT \*(Aq\*(Aq NOT NULL,
\&         class varchar(20),
\&         phylum varchar (32),          \-\- maps to \*(Aqsysgroup\*(Aq 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 \*(Aqtotal_ic\*(Aq tag
\&         sites int(3) unsigned,        \-\- not used by this module
\&         PRIMARY KEY (ID)
\&       )
\&
\&
\&       CREATE TABLE matrix_seqs (
\&         ID varchar(16) DEFAULT \*(Aq\*(Aq NOT NULL,
\&         internal varchar(8) DEFAULT \*(Aq\*(Aq 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 \*(Aq\*(Aq NOT NULL,
\&         internal varchar(8) DEFAULT \*(Aq\*(Aq NOT NULL,
\&         species varchar(24) NOT NULL,
\&         PRIMARY KEY (ID, species)
\&       )
.Ve
.PP
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 \s-1TFBS\s0 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.
.PP
\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
.SH "FEEDBACK"
.IX Header "FEEDBACK"
Please send bug reports and other comments to the author.
.SH "AUTHOR \- Boris Lenhard"
.IX Header "AUTHOR - Boris Lenhard"
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
.SS "new"
.IX Subsection "new"
.Vb 3
\& Title   : new
\& Usage   : DEPRECATED \- for backward compatibility only
\&           Use connect() or create() instead
.Ve
.SS "connect"
.IX Subsection "connect"
.Vb 10
\& 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 access permissions for
\&           the database server.
.Ve
.SS "create"
.IX Subsection "create"
.Vb 10
\& 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 access permissions
\&           for the database server.
.Ve
.SS "dbh"
.IX Subsection "dbh"
.Vb 10
\& Title   : dbh
\& Usage   : my $dbh = $db\->dbh();
\&           $dbh\->do("UPDATE matrix_data SET name=\*(AqADD1\*(Aq WHERE NAME=\*(AqSREBP2\*(Aq");
\& 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
.Ve
.SS "get_Matrix_by_ID"
.IX Subsection "get_Matrix_by_ID"
.Vb 10
\& Title   : get_Matrix_by_ID
\& Usage   : my $pfm = $db\->get_Matrix_by_ID(\*(AqM00034\*(Aq, \*(AqPFM\*(Aq);
\& 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 \*(AqPFM\*(Aq, \*(AqICM\*(Aq, and \*(AqPWM\*(Aq); 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: \*(AqPFM\*(Aq (raw position frequency matrix),
\&           \*(AqICM\*(Aq (information content matrix) or \*(AqPWM\*(Aq (position
\&           weight matrix)
\&           If Matrix_type is omitted, a PWM is retrieved by default.
.Ve
.SS "get_Matrix_by_name"
.IX Subsection "get_Matrix_by_name"
.Vb 10
\& Title   : get_Matrix_by_name
\& Usage   : my $pfm = $db\->get_Matrix_by_name(\*(AqHNF\-1\*(Aq, \*(AqPWM\*(Aq);
\& 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
\&           \*(AqPFM\*(Aq, \*(AqICM\*(Aq, and \*(AqPWM\*(Aq)
\& Args    : (Matrix_name, Matrix_type)
\&           Matrix_name is a string; Matrix_type is one of the
\&           following:
\&           \*(AqPFM\*(Aq (raw position frequency matrix),
\&           \*(AqICM\*(Aq (information content matrix) or
\&           \*(AqPWM\*(Aq (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.
.Ve
.SS "get_MatrixSet"
.IX Subsection "get_MatrixSet"
.Vb 10
\& 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, \*(AqPFM\*(Aq, \*(AqICM\*(Aq or \*(AqPWM\*(Aq
\&           \-min_ic     # float, minimum total information content
\&                       #   of the matrix
.Ve
.PP
The five arguments that expect list references are used in database
query formulation: elements within lists are combined with '\s-1OR\s0'
operators, and the lists of different types with '\s-1AND\s0'. For example,
.PP
.Vb 3
\&    my $matrixset = $db\->(\-classes => [\*(AqTRP_CLUSTER\*(Aq, \*(AqFORKHEAD\*(Aq],
\&                          \-species => [\*(AqHomo sapiens\*(Aq, \*(AqMus musculus\*(Aq],
\&                          \-matrixtype => \*(AqPWM\*(Aq);
.Ve
.PP
gives a set of PWMs whose (structural clas is '\s-1TRP_CLUSTER\s0' \s-1OR\s0
\&'\s-1FORKHEAD\s0') \s-1AND\s0 (the species they are derived from is 'Homo sapiens'
\&\s-1OR\s0 'Mus musculus').
.PP
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.
.SS "store_Matrix"
.IX Subsection "store_Matrix"
.Vb 9
\& 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
.Ve
.SS "store_MatrixSet"
.IX Subsection "store_MatrixSet"
.Vb 9
\& 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
.Ve
.SS "delete_Matrix_having_ID"
.IX Subsection "delete_Matrix_having_ID"
.Vb 9
\& Title   : delete_Matrix_having_ID
\& Usage   : $db\->delete_Matrix_with_ID(\*(AqM00045\*(Aq);
\& 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, \*(Aqdelete_Matrix_having_ID\*(Aq is a stupid name
\&           for a method, but at least it should be obviuos what it does.
.Ve