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#
# Copyright Boris Lenhard
#
# You may distribute this module under the same terms as perl itself
#
# POD
=head1 NAME
TFBS::DB::JASPAR4 - interface to MySQL relational database of pattern matrices
=head1 SYNOPSIS
=over 4
=item * creating a database object by connecting to the existing JASPAR2-type database
my $db = TFBS::DB::JASPAR4->connect("dbi:mysql:JASPAR4:myhost",
"myusername",
"mypassword");
=item * 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');
=item * 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");
=item * creating a new JASPAR4-type database named MYJASPAR4:
my $db = TFBS::DB::JASPAR4->create("dbi:mysql:MYJASPAR4:myhost",
"myusername",
"mypassword");
=item * storing a matrix in the database (currently only PFMs):
#let $pfm is a TFBS::Matrix::PFM object
$db->store_Matrix($pfm);
=back
=head1 DESCRIPTION
TFBS::DB::JASPAR4 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 JASPAR2interface, while the underlying data model is different
=head1 JASPAR2 DATA MODEL
JASPAR4 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 opseqdbtional tags.
Tags that are commonly used in the actual JASPAR database include
'medline' # PubMed ID
'species' # Species name
'superclass' #Species supergroup, eg 'vertebrate', 'plant' etc
'total_ic' # total information content - redundant, present
# for historical
'type' #experimental nethod
'acc' #accession number for TF protein sequence
'seqdb' #corresponding database name
but any tag is storable and searchable.
----------------------- ADVANCED ---------------------------------
For the developers and the curious, here is the JASPAR4 data model:
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.
-------------------------------------------------------------------------
=head1 FEEDBACK
Please send bug reports and other comments to the author.
=head1 AUTHOR - Boris Lenhard
Boris Lenhard E<lt>Boris.Lenhard@cgb.ki.seE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
=cut
# The code begins HERE:
package TFBS::DB::JASPAR4;
use vars qw(@ISA $AUTOLOAD);
# we need all three matrices due to the redundancy in JASPAR2 data model
# which will hopefully be removed in JASPAR3
use TFBS::Matrix::PWM;
use TFBS::Matrix::PFM;
use TFBS::Matrix::ICM;
use TFBS::MatrixSet;
use Bio::Root::Root;
use DBI;
# use TFBS::DB; # eventually
use strict;
@ISA = qw(TFBS::DB Bio::Root::Root);
#########################################################################
# CONSTANTS
#########################################################################
use constant DEFAULT_CONNECTSTRING => "dbi:mysql:JASPAR_DEMO"; # on localhost
use constant DEFAULT_USER => "";
use constant DEFAULT_PASSWORD => "";
#########################################################################
# PUBLIC METHODS
#########################################################################
=head2 new
Title : new
Usage : DEPRECATED - for backward compatibility only
Use connect() or create() instead
=cut
sub new {
_new (@_);
}
=head2 connect
Title : connect
Usage : my $db =
TFBS::DB::JASPAR4->connect("dbi:mysql:DATABASENAME:HOSTNAME",
"USERNAME",
"PASSWORD");
Function: connects to the existing JASPAR4-type database and
returns a database object that interfaces the database
Returns : a TFBS::DB::JASPAR4 object
Args : a standard database connection triplet
("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")
In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
use the actual values. PASSWORD and USERNAME might be
optional, depending on the user's acces permissions for
the database server.
=cut
sub connect {
# a more intuitive syntax for the constructor
my ($caller, @connection_args) = @_;
$caller->new(-connect => \@connection_args);
}
=head2 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 $db; THIS IS USED FOR WRITING NEW METHODS
FOR DIRECT RELATIONAL DATABASE MANIPULATION - if you
have write access AND do not know what you are doing,
you can severely corrupt the data
For documentation about database handle methods, see L<DBI>
Returns : the database (DBI) handle of the MySQL JASPAR2-type
relational database associated with the TFBS::DB::JASPAR2
object
Args : none
=cut
sub dbh {
my ($self, $dbh) = @_;
$self->{'dbh'} = $dbh if $dbh;
return $self->{'dbh'};
}
=head2 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; $@ contents on failure
(this is too C-like and may change in future versions)
Args : (PFM_object)
A TFBS::Matrix::PFM, FBS::Matrix::PWM or FBS::Matrix::ICM object.
PFM object are recommended to use, as they are eaily converted to
other formats
Comment : this is an experimental method that is not 100% bulletproof;
use at your own risk
=cut
sub store_Matrix {
my ($self, @PFMs) = @_;
my $err;
foreach my $pfm (@PFMs) {
eval {
$self->_store_matrix_data($pfm);
$self->_store_matrix_info($pfm);
$self->_store_matrix_annotation($pfm);
#$self->_store_matrix_species($pfm);
};
}
return $@;
}
sub create {
my ($caller, $connectstring, $user, $password) = @_;
if ($connectstring
and $connectstring =~ /dbi:mysql:(\w+)(.*)/)
{
# connect to the server;
my $dbh=DBI->connect("dbi:mysql:mysql".$2,
$user,$password)
or die("Error connecting to the database");
# create database and open it
$dbh->do("create database $1")
or die("Error creating database.");
$dbh->do("use $1");
# create tables
_create_tables($dbh);
$dbh->disconnect;
# run "new" with new database
return $caller->new(-connect=>[$connectstring, $user, $password]);
}
else {
die("Missing or malformed connect string for ".
"TFBS::DB::JASPAR2 connection.");
}
}
=head2 get_Matrix_by_ID
Title : get_Matrix_by_ID
Usage : my $pfm = $db->get_Matrix_by_ID('M00034', 'PFM');
Function: fetches matrix data under the given ID from the
database and returns a TFBS::Matrix::* object
Returns : a TFBS::Matrix::* object; the exact type of the
object depending on what form the matrix is stored
in the database (PFM is default)
Args : (Matrix_ID)
Matrix_ID is a string;
=cut
sub get_Matrix_by_ID {
my ($self, $ID, $mt) = @_;
$mt = (uc($mt) or "PWM");
unless (defined $ID) {
$self->throw("No ID passed to get_Matrix_by_ID");
}
my $matrixobj;
{
no strict 'refs';
my $ucmt = uc $mt;
my $matrixstring = $self->_get_matrixstring($ID) || return undef;
# get type of matrix
my $sth=$self->dbh->prepare(qq{SELECT type FROM MATRIX_INFO WHERE ID = '$ID'});
$sth->execute();
my $type=$sth->fetchrow_array();
# get reast of annotation as tags
$sth=$self->dbh->prepare(qq{SELECT tag, val FROM MATRIX_ANNOTATION WHERE ID = '$ID' });
$sth->execute();
my %tags;
while ( my($tag, $val)= $sth->fetchrow_array()){
$tags{$tag}=$val;
}
my $name= $tags{'name'};
my $class= $tags{'class'};
delete ($tags{'name'});
delete ($tags{'class'});
eval ("\$matrixobj= TFBS::Matrix::$type->new".'
( -ID => $ID."",
-name =>$name,
-class => $class,
-tags => \%tags,
-matrixstring=> $matrixstring # FIXME - temporary
);');
#if ($@) {$self->throw($@); }
#print "ref:",ref ($matrixobj);
}
# print $matrixobj->ID();
# print "here\n";print $matrixobj->prettyprint();
return ($matrixobj);
}
=head2 get_Matrix_by_name
Title : get_Matrix_by_name
Usage : my $pfm = $db->get_Matrix_by_name('HNF-1');
Function: fetches matrix data under the given name from the
database and returns a TFBS::Matrix::* object
Returns : a TFBS::Matrix::* object; the exact type of the object
depending on what form the matrix object was stored in
the database (default PFM))
Args : (Matrix_name)
Warning : According to the current JASPAR4 data model, name is
not necessarily a unique identifier. In the case where
there are several matrices with the same name in the
database, the function fetches the first one and prints
a warning on STDERR. You've been warned.
=cut
sub get_Matrix_by_name {
my ($self, $name, $mt) = @_;
unless(defined $name) {
$self->throw("No name passed to get_Matrix_by_name."); }
my @IDlist = $self->_get_IDlist_by_query(-name=>[$name]);
my $ID= ($IDlist[0]
or $self->warn("No matrix with name $name found."));
if ((my $L= scalar @IDlist) > 1) {
$self->warn("There are $L matrices with name '$name'");
}
return $self->get_Matrix_by_ID($ID);
}
=head2 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.
Note that this is different from JASPAR2. As any tag is supported for
database storage, any tag can be used for information retrieval.
Additionally, arguments as 'name' and 'class' can be used (even though
they are not tags.
As with get_Matrix methods, it is important to realize that any matrix
format can be stored in the database: the TFBS::MatrixSet might therefore
consist of PFMs, ICMs and PWMS, depending on how matrices are stored,
Examples include
-ID # a reference to an array of IDs (strings)
-name # a reference to an array of
# transcription factor names (string)
-class # a reference to an array of
# structural class names (strings)
-species # a reference to an array of
# Latin species names (strings)
-sysgroup # a reference to an array of
# higher taxonomic categories (strings)
-min_ic # float, minimum total information content
# of the matrix. IMPORTANT:if retrieved matrices are in PWM
format there is no way to measureinformation content.
-matrixtype #string describing type of matrix to retrieve. If left out, the format
will revert to the database format. Note that this option only works
if the database format 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 = $db->(-class => ['TRP_CLUSTER', 'FORKHEAD'],
-species => ['Homo sapiens', 'Mus musculus'],
);
gives a set of TFBS::Matrix::PFM objects (given that the matrix models are stored as such)
whose (structural clas is 'TRP_CLUSTER' OR'FORKHEAD') AND (the species they are derived
from is 'Homo sapiens'OR 'Mus musculus').
The -min_ic filter is applied after the query in the sense that the
matrices profiles with total information content less than specified
are not included in the set.
=cut
sub get_MatrixSet {
my ($self, %args) = @_;
my @IDlist = $self->_get_IDlist_by_query(%args);
my $type;
my $matrixset = TFBS::MatrixSet->new();
foreach (@IDlist) {
# print "$_\n";
}
foreach (@IDlist) {
#next if (defined $args{'-min_ic'}
# and $_->_get_total_ic($_) < $args{'-min_ic'});
#evaluate total information content: ivolves actually retrieving matrix
# is actually a problem if matrix is stored PWM: thro an error if so
my $matrix=$self->get_Matrix_by_ID($_);
#evaluate
#ugly code:
if (defined $args{'-min_ic'} ){
if ($matrix->isa("TFBS::Matrix::PFM")){
next if ( $matrix->to_ICM->total_ic() < $args{'-min_ic'});
}
if ($matrix->isa("TFBS::Matrix::ICM")){
next if ($matrix->total_ic() < $args{'-min_ic'});
}
if ($matrix->isa("TFBS::Matrix::PWM")){
$self->throw("Cannot evaluate information constent from PWM matrices");
}
}
#ugly code:
if ($args{'-matrixtype'} && $matrix->isa("TFBS::Matrix::PFM")){
if ( $args{'-matrixtype'} eq ('PWM')) {
# warn "change";
$matrix= $matrix->to_PWM();
}
if ( $args{'-matrixtype'} eq ('ICM')) {
#warn "change";
$matrix= $matrix->to_PWM();
}
}
$matrixset->add_Matrix($matrix);
}
return $matrixset;
}
sub store_MatrixSet {
$_[0]->throw ("Method store_MtrixSet not yet implemented.");
}
=head2 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; $@ contents on failure
(this is too C-like and may change in future versions)
Args : (ID)
A string
Comment : Yeah, yeah, 'delete_Matrix_having_ID' is a stupid name
for a method, but at least it should be obviuos what it does.
=cut
sub delete_Matrix_having_ID {
my ($self, @IDs) = @_;
eval {
foreach my $ID (@IDs) {
my $q_ID = $self->dbh->quote($ID);
foreach my $table (qw (MATRIX_DATA
MATRIX_INFO
MATRIX_ANNOTATION
)
)
{
$self->dbh->do("DELETE from $table where ID=$q_ID");
}
}
};
return $@;
}
#########################################################################
# PRIVATE METHODS
#########################################################################
sub _new {
my ($caller, %args) = @_;
my $class = ref $caller || $caller;
my $self = bless {}, $class;
my ($connectstring, $user, $password);
if ($args{'-connect'} and (ref($args{'-connect'}) eq "ARRAY")) {
($connectstring, $user, $password) = @{$args{'-connect'}};
}
elsif ($args{'-create'} and (ref($args{'-create'}) eq "ARRAY")) {
return $caller->create(@{-args{'create'}});
}
else {
($connectstring, $user, $password) =
(DEFAULT_CONNECTSTRING, DEFAULT_USER, DEFAULT_PASSWORD);
}
$self->dbh( DBI->connect($connectstring, $user, $password) );
return $self;
}
sub _store_matrix_data {
my ($self, $pfm, $ACTION) = @_;
my @base = qw(A C G T);
my $matrix = $pfm->matrix();
my $type;
my $sth = $self->dbh->prepare
(q! INSERT INTO MATRIX_DATA VALUES(?,?,?,?) !);
for my $i (0..3) {
for my $j (0..($pfm->length-1)) {
$sth->execute( $pfm->ID,
$base[$i],
$j+1,
$matrix->[$i][$j]
)
or $self->throw("Error executing query.");
}
}
}
sub _store_matrix_info {
my ($self, $pfm, $ACTION) = @_;
my $type;
$type= 'PFM' if $pfm->isa("TFBS::Matrix::PFM");
$type= 'PWM' if $pfm->isa("TFBS::Matrix::PWM");
$type= 'ICM' if $pfm->isa("TFBS::Matrix::ICM");
my $sth = $self->dbh->prepare
(q! INSERT INTO MATRIX_INFO
(ID, type)
VALUES(?,?) !);
$sth->execute($pfm->ID,
$type,
)
or $self->throw("Error executing query");
}
sub _store_matrix_annotation {
my ($self, $pfm, $ACTION) = @_;
my $sth = $self->dbh->prepare
(q! INSERT INTO MATRIX_ANNOTATION
(ID, tag, val)
VALUES(?,?,?) !);
$sth->execute($pfm->ID,
'name',
($pfm->name() or ""),
);
$sth->execute($pfm->ID,
'class',
($pfm->class() or ""),
);
# get all tags
my %tags= $pfm->all_tags();
foreach my $tag( keys %tags){
$sth->execute($pfm->ID,
$tag,
($tags{$tag} or ""),
)
or $self->throw("Error executing query");
}
}
#when creating: try to support arbitrary tags
sub _create_tables {
# utility function
# If you want to change the databse schema,
# this is the right place to do it
my $dbh = shift;
my @queries =
(
q!
CREATE TABLE MATRIX_DATA(
ID VARCHAR (16) DEFAULT '' NOT NULL,
row VARCHAR(1) NOT NULL,
col TINYINT(3) UNSIGNED NOT NULL,
val FLOAT,
PRIMARY KEY (ID, row, col)
)
!,
q!
CREATE TABLE MATRIX_INFO(
ID VARCHAR (16) DEFAULT '' NOT NULL PRIMARY KEY ,
type ENUM ('PFM', 'ICM','PWM') DEFAULT 'PFM' NOT NULL
)
!,
q!
CREATE TABLE MATRIX_ANNOTATION(
ID VARCHAR (16) DEFAULT '' NOT NULL,
tag VARCHAR(255) DEFAULT '' NOT NULL,
val TEXT,
PRIMARY KEY (ID, tag)
)
!,
);
foreach my $query (@queries) {
$dbh->do($query)
or die("Error executing the query: $query\n");
}
}
sub _get_matrixstring {
my ($self, $ID) = @_;
#my %dbname = (PWM => 'pwm', PFM => 'raw', ICM => 'info');
#unless (defined $dbname{$mt}) {
#$self->throw("Unsupported matrix type: ".$mt);
#}
my $sth;
my $qID = $self->dbh->quote($ID);
my $matrixstring = "";
foreach my $base (qw(A C G T)) {
$sth=$self->dbh->prepare
("SELECT val FROM MATRIX_DATA
WHERE ID=$qID AND row='$base' ORDER BY col");
$sth->execute;
$matrixstring .=
join (" ", (map {$_->[0]} @{$sth->fetchall_arrayref()}))."\n";
}
$sth->finish;
return undef if $matrixstring eq "\n"x4;
return $matrixstring;
}
sub _get_IDlist_by_query {
# called by get_MatrixSet
# should be able to search for arbitrary tags...hmmm
my ($self, %args) = @_;
my ($TABLES, %arrayref);
my (%intersected_set);
foreach my $key(keys %args){
unless ( $key eq "-min_ic" or $key eq "-matrixtype"){
my $oldkey=$key;
$key=~s/-//;
$arrayref{$key}= $args{$oldkey};
}
}
my @andconditions;
$TABLES = 'MATRIX_ANNOTATION ';
#special case: get all matrices
unless (keys %arrayref){
my $query = "SELECT DISTINCT ID FROM $TABLES ";
my $sth = $self->dbh->prepare($query);
$sth->execute() or $self->throw("Query failed:\n$query\n");
my @ary;
while (my ($id) = $sth->fetchrow_array()) {
push (@ary, $id);
}
return(@ary);
}
foreach my $key (keys %arrayref) {
#print "key: $key\n";
if ($key eq 'ID'){
push @andconditions,
"(".
join(" OR ",
(map {"MATRIX_ANNOTATION.ID=".
$self->dbh->quote($_)
}
@{$arrayref{$key}}
)).
")";
}
else{
push @andconditions,
"(".
join(" OR ",
(map {"MATRIX_ANNOTATION.tag=". $self->dbh->quote($key)." AND val=".
$self->dbh->quote($_)
}
@{$arrayref{$key}}
)).
")";
}
push (@andconditions, 1) unless(@andconditions);
my $WHERE = ((scalar @andconditions) == 0) ? "" : " WHERE ";
my $query =
"SELECT DISTINCT ID FROM $TABLES $WHERE".
join(" AND ", @andconditions);
# warn $query;
undef @andconditions;
my $sth = $self->dbh->prepare($query);
$sth->execute() or $self->throw("Query failed:\n$query\n");
# collect IDs and return
my %current_query;
while (my ($id) = $sth->fetchrow_array()) {
$current_query{$id}=1;
}
unless (%intersected_set){
%intersected_set= %current_query;
next;
}
# do intersect
foreach my $key (keys %intersected_set){
delete $intersected_set{ $key} unless $current_query{$key};
}
}
my @ary;
foreach my $key (keys %intersected_set){
push (@ary, $key);
# warn "$key\n";
}
return (@ary);
}
sub DESTROY {
$_[0]->dbh->disconnect() if $_[0]->dbh;
}
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