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#!/usr/bin/perl -w
# viewpfm.cgi
# by Boris Lenhard
#
# See POD documentation for this CGI script at the end of the file
#
use strict;
use CGI ();
use TFBS::Matrix::PFM;
use TFBS::DB::FlatFileDir;
use constant DATABASE_DIR => "examples/SAMPLE_FlatFileDir";
# The directory to store created logo image: we need an absolute
# path for access by the script, and a relative path for
# access by the web browser
use constant ABSOLUTE_IMAGE_DIR => "/var/www/html/TEMP";
use constant RELATIVE_IMAGE_DIR => "/TEMP";
use constant THIS_SCRIPT => "/cgi-bin/viewpfm.cgi";
# IMPORTANT NOTE: this script does not delete image files it creates
# page
# connect to FlatFileDir matrix database
# (there is a sample FlatFileDir matrix database directory
# examples/SAMPLE_FlatFileDir in the TFBS distribution package)
# Change this line if you want to use a different type of database
# (e.g. TFBS::DB::JASPAR2)
my $db = TFBS::DB::FlatFileDir->connect(DATABASE_DIR);
if (CGI::param("matrix_id")) { # matrix entry
matrix_info($db, CGI::param("matrix_id"));
}
else { # draw logo
matrix_list_page($db);
}
sub matrix_list_page {
my ($db) = @_;
my $q = CGI->new;
# get all matrices (TFBS::Matrix::PWM objects) into a TFBS::MatrixSet object
my $matrixset = $db->get_MatrixSet(-matrixtype=>"PFM");
print $q->header, $q->start_html;
print $q->h1("Matrices in the database");
my $matrix_iterator = $matrixset->Iterator(-sort_by=>"ID");
my @table_rows = ($q->Tr($q->th([ 'MatrixID', 'Name',
'Class','Length', 'Total IC'])));
while (my $pfm = $matrix_iterator->next) {
push @table_rows,
$q->Tr($q->td([$q->a({-href=>THIS_SCRIPT."?matrix_id=".$pfm->ID},
$pfm->ID),
$pfm->name, $pfm->class,
$pfm->length, $pfm->to_ICM->total_ic]));
}
print $q->table({-border=>1}, @table_rows);
print $q->end_html;
}
sub matrix_info {
my ($db, $matrix_id) = @_;
my $q = CGI->new;
my $pfm = $db->get_matrix_by_ID($matrix_id);
unless(defined $pfm) {
# first we draw a sequence logo and store it in a .png file
my $logofile = $pfm->ID.".png";
# we want image size to vary with motif length:
my $xsize = 60+20*$pfm->length();
# ...but it should not be too narrow for short motifs:
$xsize=278 if($pfm->length()<10);
$pfm->draw_logo(-file =>ABSOLUTE_IMAGE_DIR."/$logofile",
-full_scale =>2.25,
-xsize =>$xsize,
-ysize =>190,
-graph_title=> $pfm->name,
-x_title=>"Nucleotide position",
-y_title=>"ic [bits]");
# then we output the page
print $q->header, $q->start_html;
print $q->div("Matrix ID : ".$pfm->ID);
print $q->div("Transctiption factor name : ", $pfm->name);
print $q->div("Structural class : ", $pfm->class);
print $q->div("Total information content : ",
sprintf("%2.2f",$pfm->to_ICM->total_ic));
print $q->div("Matrix:");
print $q->div($q->pre($pfm->prettyprint));
print $q->div("Sequence logo:");
print $q->img({-src=>RELATIVE_IMAGE_DIR."/$logofile"});
print $q->div($q->a({-href=>THIS_SCRIPT}, "Back to matrix list"));
print $q->end_html;
}
else { # matrix not found
print $q->header, $q->start_html;
print $q->h2("Matrix $matrix_id not found in the database");
print $q->a({-href=>THIS_SCRIPT}, "Back to matrix list");
print $q->end_html;
}
}
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