TFBS::DB::JASPAR2(3pm)

NAME

TFBS::DB::JASPAR2 - interface to MySQL relational database of pattern
matrices

SYNOPSIS

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

        my $db = TFBS::DB::JASPAR2->connect("dbi:mysql:JASPAR2:myhost",
                                            "myusername",
                                            "mypassword");

o   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');

o   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");

o   creating a new JASPAR2-type database named MYJASPAR2:

        my $db = TFBS::DB::JASPAR2->create("dbi:mysql:MYJASPAR2:myhost",
                                           "myusername",
                                           "mypassword");

o   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.

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