TFBS::DB
JASPAR2
TFBS::DB::JASPAR2 - interface to MySQL relational database of pattern matrices
|
| Globals (from use vars definitions) |
| $AUTOLOAD |
TFBS::DB::JASPAR2 is a read/write database interface module that
retrieves and stores TFBS::Matrix::* and TFBS::MatrixSet
objects in a relational database.
|
Methods description
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.
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.
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:
-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.
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.
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.
Title : new
Usage : DEPRECATED - for backward compatibility only
Use connect() or create() instead
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
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; $@ contents on failure
(this is too C-like and may change in future versions)
Args : (MatrixSet_object)
A TFBS::MatrixSet object
Comment : THIS METHOD IS NOT YET IMPLEMENTED
Methods code
sub AUTOLOAD
{ my ($self, $ID) = @_;
no strict 'refs';
my $TABLE;
my %dbname_of = (ID => 'ID',
name => 'name',
class => 'class',
species => 'species',
sysgroup => 'phylum',
type => 'type',
seqdb => 'seq_db',
acc => 'seq',
total_ic => 'IC',
medline => 'medline'
);
my ($where_column, $where_value);
if ($AUTOLOAD =~ /.*::_{0,1}get_(\w+)_list/) {
defined $dbname_of{$1} or $self->throw("$AUTOLOAD: no such method!");
($where_column, $where_value) = (1,1);
}
elsif ($AUTOLOAD =~ /.*::_get_(\w+)/) {
defined $dbname_of{$1} or $self->throw("$AUTOLOAD: no such method!");
defined $ID or $self->throw("No ID provided for $AUTOLOAD");
($where_column, $where_value) = ('ID', $ID);
}
else {
$self->throw("$AUTOLOAD: no such method!");
}
defined $dbname_of{$1} or $self->throw("$AUTOLOAD: no such method!");
if ($1 eq 'species') { $TABLE = 'matrix_species'; }
elsif ($1 eq 'seqdb' or $1 eq 'acc') { $TABLE = 'matrix_seqs', }
else { $TABLE = 'matrix_info' ; }
my @results = $self->_simple_query ($TABLE, $dbname_of{$1},
$where_column => $where_value);
wantarray ? return @results : return $results[0];}
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,
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,
pwm float(7,5),
normalized float(7,5) unsigned,
PRIMARY KEY (pos_ID),
KEY id_index (ID)
)
!,
q!!
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),
litt varchar(40),
medline int(12),
information varchar(20),
iterations varchar(6),
width int(2),
consensus varchar(25),
IC float(6,4),
sites int(3) unsigned,
PRIMARY KEY (ID)
)
!,
q!!
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)
)
!,
q!!
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)
)
!);
foreach my $query (@queries) {
$dbh->do($query)
or die("Error executing the query: $query\n");
}
}
sub _get_IDlist_by_query
{
## called by get_MatrixSet
my ($self, %args) = @_;
my ($TABLES, %arrayref);
$args{-names} and $arrayref{name} = $args{-names} ;
$args{-classes} and $arrayref{class} = $args{-classes} ;
$args{-sysgroups} and $arrayref{phylum} = $args{-sysgroups};
$args{-IDs} and $arrayref{ID} = $args{-IDs};
my @andconditions;
if ($args{-species}) {
$TABLES = ' matrix_info, matrix_species ';
push @andconditions,
'matrix_info.ID = matrix_species.ID',
" (".
join(" OR ",
(map {"matrix_species.species=".
$self->dbh($_)
}
@{$args{-species}}
)).
") ";
}
else {
$TABLES = 'matrix_info ';
}
foreach my $key (keys %arrayref) {
if (scalar @{$arrayref{$key}}) {
push @andconditions,
"(".
join(" OR ",
(map {"matrix_info.$key=".
$self->dbh($_)
}
@{$arrayref{$key}}
)).
")";
}
else {
push @andconditions, "(1=0)";
}
}
my $WHERE = ((scalar @andconditions) == 0) ? "" : " WHERE ";
my $query =
"SELECT DISTINCTROW matrix_info.id FROM $TABLES $WHERE".
join(" AND ", @andconditions);
my $sth = $self->dbh($query);
$sth->execute() or $self->throw("Query failed:\n$query\n");
## collect IDs and return
my @IDlist = ();
while (my ($id) = $sth->fetchrow_array()) {
push @IDlist, $id;
}
$sth->finish;
return @IDlist;}
sub _get_matrixstring
{ my ($self, $ID, $mt) = @_;
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 $dbname{$mt} FROM matrix_data
WHERE ID=$qID AND base='$base' ORDER BY position");
$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 $self;}
sub _simple_query
{ my ($self, $table, $retr_field, $search_field, $search_value) = @_;
my $q_value = $self->dbh($search_value);
my $sth = $self->dbh->prepare
("SELECT DISTINCT $retr_field from $table WHERE $search_field = $q_value and $retr_field <>\"\" ORDER BY $retr_field");
$sth->execute;
return (map {$_->[0]} @{$sth->fetchall_arrayref});}
sub _store_matrix_data
{ my ($self, $pfm, $ACTION) = @_;
my @base = qw(A C G T);
my $pfmatrix = $pfm->matrix();
my $icmatrix = $pfm->to_ICM()->matrix();
my $pwmatrix = $pfm->to_PWM();
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,
$pfm->ID.".".$base[$i].".".($j+1),
$base[$i],
$j+1,
$pfmatrix->[$i][$j],
$icmatrix->[$i][$j],
$pwmatrix->[$i][$j],
$pfmatrix->[$i][$j] / $pfm->column_sum())
or $self->throw("Error executing query.");
}
}}
sub _store_matrix_info
{ my ($self, $pfm, $ACTION) = @_;
my $sth = $self->dbh->prepare
(q!! INSERT INTO matrix_info
(ID, name, type, class, phylum, width, IC, sites)
VALUES(?,?,?,?,?,?,?,?) !);
$sth->execute($pfm->ID,
($pfm->name or $pfm->ID),
($pfm->{'tags'}->{'type'} or ""),
($pfm->class() or undef),
($pfm->{'tags'}->{'sysgroup'} or undef),
$pfm->length(),
$pfm->to_ICM(),
$pfm->column_sum()
)
or $self->throw("Error executing query");}
sub _store_matrix_seqs
{ my ($self, $pfm, $ACTION) = @_;
return unless ($pfm->{'tags'}->{'seqdb'} or $pfm->{'tags'}->{'acc'});
my $sth = $self->dbh->prepare
(q!! INSERT INTO matrix_seqs
(ID, seq_db, seq)
VALUES(?,?,?) !);
$sth->execute($pfm->ID,
($pfm->{'tags'}->{'seqdb'} or ""),
($pfm->{'tags'}->{'acc'} or "")
)
or $self->throw("Error executing query");}
sub _store_matrix_species
{ my ($self, $pfm, $ACTION) = @_;
return unless $pfm->{'tags'}->{'species'};
my $sp = $pfm->{'tags'}->{'species'};
my @splist = (ref($sp) ? @$sp : $sp);
foreach my $species (@splist) {
my $sth = $self->dbh->prepare
(q!! INSERT INTO matrix_species
(ID, species)
VALUES(?,?) !);
$sth->execute($pfm->ID,
$species
)
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_seqs
matrix_species)
)
{
$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 $mt = ($args{'-matrixtype'} or "PWM");
my $matrixset = TFBS::MatrixSet->new();
foreach (@IDlist) {
next if (defined $args{'-min_ic'}
and $self->_get_total_ic($_) < $args{'-min_ic'});
$matrixset->add_Matrix($self->get_Matrix_by_ID($_, $mt));
}
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, $mt) || return undef;
eval("\$matrixobj= TFBS::Matrix::$ucmt->new".'
( -ID => $ID,
-name => $self->_get_name($ID)."",
-class => $self->_get_class($ID)."",
-tags => { "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"=> ($self->_get_total_ic($ID) or "")
},
-matrix=> $matrixstring # FIXME - temporary
);');
if ($@) {$self->throw($@); }
}
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 = $self->_get_IDlist_by_query(-names=>[$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, $mt);}
sub new
{ _new (@_);
}
sub store_Matrix
{ my ($self, @PFMs) = @_;
my $err;
foreach my $pfm (@PFMs) {
eval {
$self->_store_matrix_data($pfm);
$self->_store_matrix_info($pfm);
$self->_store_matrix_seqs($pfm);
$self->_store_matrix_species($pfm);
};
}
return $@;}
sub store_MatrixSet
{ $_[0]->throw ("Method store_MtrixSet not yet implemented.");}
General documentation
| JASPAR2 DATA MODEL |
top |
JASPAR2 is working name for a relational database model used
for storing transcriptional factor pattern matrices in a MySQL database.
It was initially designed to store matrices for the JASPAR database of
high quality eukaryotic transcription factor specificity profiles by
Albin Sandelin and Wyeth W. Wasserman. Besides the profile matrix itself,
this data model stores profile ID (unique), name, structural class,
basic taxonomic and bibliographic information
as well as some additional optional tags.
Due to its data model, which precedeed the design of the
module, TFBS::DB::JASPAR2 cannot store arbitrary tags for a matrix.
The supported tags are
'acc' # (accession number;
# originally for transcription factor protein seq)
'seqdb' # sequence database where 'acc' comes from
'medline' # PubMed ID
'species' # Species name
'sysgroup'
'total_ic' # total information content - redundant, present
# for historical
"medline" => ($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 |
top |
Please send bug reports and other comments to the author.
|
| AUTHOR - Boris Lenhard |
top |
Boris Lenhard Boris.Lenhard@cgb.ki.seEi.se>
|
| APPENDIX |
top |
The rest of the documentation details each of the object
methods. Internal methods are preceded with an underscore.
|