.\" Automatically generated by Pod::Man 4.10 (Pod::Simple 3.35) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "TFBS::DB::JASPAR2 3pm" .TH TFBS::DB::JASPAR2 3pm "2018-11-02" "perl v5.28.0" "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 .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 acces 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 acces 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 \& 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