TFBS::DB
LocalTRANSFAC
TFBS::DB::LocalTRANSFAC - interface to local transfac database
position frequency matrices (matrix.dat)
-------------------------------- NOTICE ----------------------------------
The TRANSFAC database is free for non-commercial use. For commercial use
the TRANSFAC databases and programs have to be licensed. Please read
the DISCLAIMER at http://transfac.gbf.de/TRANSFAC/disclaimer.htm.
-------------------------------------------------------------------------
|
| No package variables defined. |
TFBS::DB::LocalTRANSFAC is a read only database interface that fetches
TRANSFAC matrix data from a local TRANSFAC install (matrix.dat)
|
Methods description
Title : connect
Usage : my $db = TFBS::DB::TRANSFAC->connect(%args);
Function: Creates a TRANSFAC database connection object, which can be used
to retrieve matrices from a locally installed TRANSFAC database
Returns : a TFBS::DB::TRANSFAC object
Args : -localdir # REQUIRED: the directory of the matrix.dat TRANSFAC
# datafile. matrix.dat must have read access.
-accept_conditions # OPTIONAL: by setting this to a true
# value, you confirm that you
# have read and accepted the terms
# of use of TRANSFAC at
# http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
# this also supresses the annoying
# message that is printed to STDERR
# upon invoking the method
Title : get_Matrix_by_ID
Usage : my $pfm = $db->get_Matrix_by_ID('V$CREB_01', 'PFM');
Function: fetches matrix data under the given TRANSFAC 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 PFM is retrieved by default.
Title : get_Matrix_by_acc
Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');
Function: fetches matrix data under the given TRANSFAC aaccession number
from 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 PFM is retrieved by default.
Methods code
| _get_Matrix_Block | description | top | prev | next |
sub _get_Matrix_Block
{ my %params = @_;
my $loc = $params{'loc'};
my $acc = $params{'acc'};
my $ID = $params{'ID'};
$loc = $loc . "/matrix.dat";
open(HANDLE, $loc) || die ("File opening failed for matrix.dat: Check file permissions");
my @raw_data=<HANDLE>;
my @block = ();
my $hit = 0;
foreach my $line (@raw_data)
{
if ($line eq "//\n")
{
foreach my $lineinblock (@block)
{
if (defined $ID) {
if ($lineinblock eq "ID $ID\n") { $hit = 1 };
}
if (defined $acc) {
if ($lineinblock eq "AC $acc\n") { $hit = 1 };
}
}
if ($hit == 0) { @block = (); }
}
if ($hit == 0) { push @block, $line; }
}
close(HANDLE);
return\@ block;}
sub _get_Matrix_by_Block
{ my ($self, $datablock, $mt) = @_;
my @datalines = @$datablock;
my (@As, @Cs, @Gs, @Ts, $name, $ID, $acc);
foreach my $line (@datalines)
{
if ($line =~ /NA\s+(\S+)\n/) {
$name = $1;
}
if ($line =~ /ID\s+(\S+)\n/) {
$ID = $1;
}
if ($line =~ /AC\s+(\S+)\n/) {
$acc = $1;
}
##if ($line =~ /\d{2}\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\n/) {
## change to allow for both older and newer file format
## contributed by Leonardo Marino-Ramirez:
## Updated 2003-09-05 to enable parsing of non-integer entries
if ($line =~ /^\d{2}\s+(\d+\.?\d*)\s+(\d+\.?\d*)\s+(\d+\.?\d*)\s+(\d+\.?\d*).*$/) {
push @As, $1;
push @Cs, $2;
push @Gs, $3;
push @Ts, $4;
}
}
return undef unless @As;
my $pfm = TFBS::Matrix::PFM-> new ( -ID => $ID,
-name => $name,
-tags => {acc=>$acc},
-matrix => [\@ As,\@ Cs,\@ Gs,\@ Ts]
);
if (!defined($mt) or uc($mt) eq "PFM") {return $pfm;}
elsif (uc($mt) eq "ICM") {return $pfm->to_ICM;}
elsif (uc($mt) eq "PWM") {return $pfm->to_PWM;}
else { $self->throw("Unrecognized matrix format: $mt"); }}
sub connect
{ my ($caller, %args) = @_;
my $self = bless { 'loc' => $args{'-localdir'}}, ref $caller || $caller;
unless (defined ($args{-accept_conditions}) and $args{-accept_conditions}) {
print STDERR <<ENDNOTICE
-------------------------------- NOTICE ----------------------------------
The TRANSFAC database is free for non-commercial use. For commercial use
the TRANSFAC databases and programs have to be licensed. Please read
the DISCLAIMER at http://transfac.gbf.de/TRANSFAC/disclaimer.htm.
-----------
If you have read the disclaimer and accept the conditions stated therein,
you can suppres this notice by connecting to TRANSFAC like this:
my\$ db = TFBS::DB::TRANSFAC->connect(-accept_conditions => 1);
--------------------------------------------------------------------------
ENDNOTICE
;
}
unless (defined $args{-localdir}) {
$self->throw("Need directory of TRANSFAC database");
}
return $self;}
sub get_Matrix_by_ID
{ my ($self, $ID, $mt) = @_;
unless (defined $ID) {
$self->throw("No parameters passed to get_Matrix_by_ID.");
}
my $datablock = _get_Matrix_Block ( 'ID' => $ID,
'loc' => $self->{'loc'});
return $self->_get_Matrix_by_Block($datablock, $mt);}
sub get_Matrix_by_acc
{ my ($self, $acc, $mt) = @_;
unless (defined $acc) {
$self->throw("No parameters passed to get_Matrix_by_ID.");
}
my $datablock = _get_Matrix_Block ( 'acc' => $acc,
'loc' => $self->{'loc'});
return $self->_get_Matrix_by_Block($datablock, $mt);}
General documentation
No general documentation available.