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TFBS::DB::JASPAR5 - interface to MySQL relational database of pattern matrices. Currently status: experimental.
· 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);
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. -------------------------------------------------------------------------
Please send bug reports and other comments to the author.
AUTHOR - Boris Lenhard
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
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; $@ 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_CLUSTER' OR'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; $@ 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.