/usr/lib/perl5/TFBS/DB/TRANSFAC.pm is in libtfbs-perl 0.5.svn.20100421-1build1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 | # TFBS module for TFBS::DB::TRANSFAC
#
# Copyright Boris Lenhard
#
# You may distribute this module under the same terms as perl itself
#
# POD
=head1 NAME
TFBS::DB::TRANSFAC - interface to database of TRANSFAC public
position frequency matrices at TESS (http://www.cbil.upenn.edu/tess)
-------------------------------- 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.
-------------------------------------------------------------------------
=head1 SYNOPSIS
=over 4
=item * creating a database object by connecting to TRANSFAC data
my $db = TFBS::DB::TRANSFAC->connect();
=item * retrieving a TFBS::Matrix::* object from the database
# retrieving a PFM by ID
my $pfm = $db->get_Matrix_by_ID('V$CEBPA_01','PFM');
#retrieving a PWM by TRANSFAC accession number
my $pwm = $db->get_Matrix_by_acc('M00116', 'PWM');
=back
=head1 DESCRIPTION
TFBS::DB::TRANSFAC is a read only database interface that fetches
TRANSFAC matrix data from TESS web interface
(http://www.cbil.upen.edu/TESS) and returns TFBS::Matrix::* objects.
=cut
package TFBS::DB::TRANSFAC;
use vars qw(@ISA $ua);
use strict;
use Bio::Root::Root;
use TFBS::Matrix::PFM;
use LWP::Simple qw($ua get);
@ISA = qw(TFBS::DB Bio::Root::Root);
=head2 connect
Title : connect
Usage : my $db = TFBS::DB::TRANSFAC->connect(%args);
Function: Creates a TRANSFAC database connection object, which can be used
to retrieve matrices from public TRANSFAC databases via the web
Returns : a TFBS::DB::TRANSFAC object
Args : -proxy # OPTIONAL: a http proxy server name,
# usually required for accessing TRANSFAC from behind
# a firewall
-accept_conditions # OPTIONAL: by setting this to a true
# value, you confirm that you
# have read and accepted the terms
# of use of TRANSFAC at
# http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
# this also supresses the annoying
# message that is printed to STDERR
# upon invoking the method
=cut
sub connect {
my ($caller, %args) = @_;
my $self = bless {}, 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
;
}
if (defined $args{'-proxy'}) {
$ua->proxy('http',$args{'-proxy'});
}
return $self;
}
=head2 new
Title : connect
Usage : my $db = TFBS::DB::TRANSFAC->connect(%args);
Function: Here, I<new> is just a synonim for I<connect>
(to make the interface consistent with other
bioperl read-obly Bio::DB::* objects)
Returns : a TFBS::DB::TRANSFAC object
Args : -accept_conditions # see explanation at I<new>
=cut
sub new {
my ($caller, %args) = @_;
$caller->connect(%args);
}
=head2 get_Matrix_by_ID
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.
=cut
sub get_Matrix_by_ID {
my ($self, $ID, $mt) = @_;
unless (defined $ID) {
$self->throw("No parameters passed to get_Matrix_by_ID.");
}
my $url = "http://www.cbil.upenn.edu/cgi-bin/tess/tess33?request=MTX-DBRTRV-Id&key=$ID";
# my $url = "http://www.cbil.upenn.edu/cgi-bin/tess/tess33?request=MTX-DBRTRV-Id&key=$ID";
return $self->_get_Matrix_by_URL($url, $mt);
}
=head2 get_Matrix_by_acc
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.
=cut
sub get_Matrix_by_acc {
my ($self, $acc, $mt) = @_;
unless (defined $acc) {
$self->throw("No parameters passed to get_Matrix_by_ID.");
}
my $url = "http://www.cbil.upenn.edu/cgi-bin/tess/tess33?request=MTX-DBRTRV-Accno&key=$acc";
return $self->_get_Matrix_by_URL($url, $mt);
}
sub get_MatrixSet {
my ($self, %args) = @_;
# not yet implemented
}
sub _get_Matrix_by_URL {
my ($self, $url, $mt) = @_;
my $HTMLpage = get $url || return undef;
my (@As, @Cs, @Gs, @Ts, $name, $ID, $acc);
my @lines = split "\n", $HTMLpage;
foreach my $line (@lines) {
$line =~ s/\r//;
$line =~ s/<\/{0,1}b>//gi;
$line =~ s/ //gi;
if ($line =~ /Name<\/td><td>([^<]+)</) {
$name = $1;
}
elsif ($line =~ /ID<\/td><td>([^<]+)</) {
$ID = $1;
}
elsif ($line =~ /AccNo\/Logo<\/td><td>([^<]+)</) {
$acc = $1;
}
elsif ($line =~ /\d+\.\d+\s+(\d+\.\d+)\s+(\d+\.{0,1}\d*)\s+(\d+\.{0,1}\d*)\s+(\d+\.{0,1}\d*)\s+(\d+\.{0,1}\d*)/) {
my ($nr, $A, $C, $G, $T) = ($1,$2,$3,$4,$5); #split /\s+/, $line;
push @As,$A; push @Cs,$C; push @Gs,$G; push @Ts,$T;
}
}
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"); }
}
1;
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