TFBS::DB
JASPAR4
TFBS::DB::JASPAR4 - interface to MySQL relational database of pattern matrices
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| Globals (from use vars definitions) |
| $AUTOLOAD |
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
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Methods description
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.
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 DBI
Returns : the database (DBI) handle of the MySQL JASPAR2-type
relational database associated with the TFBS::DB::JASPAR2
object
Args : none
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.
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 taht 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 infromation content less than specified
are not included in the set.
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;
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.
Title : new
Usage : DEPRECATED - for backward compatibility only
Use connect() or create() instead
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
Methods code
sub DESTROY
{ $_[0]->dbh() if $_[0]->dbh;
}
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(7,4),
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 varchar(255) DEFAULT '',
PRIMARY KEY (ID, tag)
)
!,
);
foreach my $query (@queries) {
$dbh->do($query)
or die("Error executing the query: $query\n");
}
}
sub _get_IDlist_by_query
{
## called by get_MatrixSet
## should be able to search for arbitrary tags...hmmm
my ($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 = $self->dbh($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=".
$self->dbh($_)
}
@{$arrayref{$key}}
)).
")";
}
else{
push @andconditions,
"(".
join(" OR ",
(map {"MATRIX_ANNOTATION.tag=". $self->dbh($key)." AND val=".
$self->dbh($_)
}
@{$arrayref{$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 = $self->dbh($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 _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 = $self->dbh($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 $matrixstring;}
sub _new
{ my ($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 $self;}
sub _store_matrix_annotation
{ my ($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 $self->throw("Error executing query");
}}
sub _store_matrix_data
{ my ($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 $self->throw("Error executing query");}
sub connect
{ ## a more intuitive syntax for the constructor
my ($caller, @connection_args) = @_;
$caller->new(-connect =>\@ connection_args);
}
sub create
{ my ($caller, $connectstring, $user, $password) = @_;
if ($connectstring
and $connectstring =~ /dbi:mysql:(\w+)(.*)/)
{
## connect to the server;
my $dbh=DBI("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, $password]);
}
else {
die("Missing or malformed connect string for ".
"TFBS::DB::JASPAR2 connection.");
}}
sub dbh
{ my ($self, $dbh) = @_;
$self->{'dbh'} = $dbh if $dbh;
return $self->{'dbh'};}
sub delete_Matrix_having_ID
{ my ($self, @IDs) = @_;
eval {
foreach my $ID (@IDs) {
my $q_ID = $self->dbh($ID);
foreach my $table (qw (MATRIX_DATA
MATRIX_INFO
MATRIX_ANNOTATION
)
)
{
$self->dbh("DELETE from $table where ID=$q_ID");
}
}
};
return $@;}
sub get_MatrixSet
{ my ($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() < $args{'-min_ic'});
}
if ($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 $matrixset;}
sub get_Matrix_by_ID
{
my ($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(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(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);}
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);}
sub new
{ _new (@_);
}
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 $@;}
| store_MatrixSet | description | top | prev | next |
sub store_MatrixSet
{ $_[0]->throw ("Method store_MtrixSet not yet implemented.");}
General documentation
| JASPAR2 DATA MODEL |
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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.
-------------------------------------------------------------------------
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| FEEDBACK |
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Please send bug reports and other comments to the author.
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| AUTHOR - Boris Lenhard |
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Boris Lenhard Boris.Lenhard@cgb.ki.seEi.se>
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| APPENDIX |
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The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
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