#!/tools/bin/perl
#####################################################################
# grape.cgi - checks grid alignment between slides, works
# with QuantArray, Dapple and DigitalGENOME output files
#
# Checks first line in quantitation file to determine spotfinder used,
# should ID QuantArray and digitalGENOME correctly, assumes anything
# else is dapple
#
# Determines if there is a better alignment by shifting the grid
# up to 1/8 of total # of spots in each dimension x and y
#
# Created: 2001 Bruz Marzolf
#
# Last Modified: May 21, 2003
#
#####################################################################
use Benchmark;
use strict;
use CGI qw(:standard);
use PDL;
use PDL::Fit::Polynomial;
require 'quantitation.pl';
my $DEBUG = 0;
# list of quantitation files
my @quantFiles;
$| = 1; # flush print output immediately
print header,
start_html( -title=>'Institute for Systems Biology - GrAPE');
print_grape_header();
if ( param("Check") ) {
print_table();
}
elsif ( param("Find Files") ) {
get_quant_list();
choose_files();
}
else {
#print_grape_info();
print_login_page();
}
print_grape_footer();
print end_html;
#########################
# Form Subs
#########################
sub print_grape_info {
print << "EndInfo"
GrAPE is a tool that analyzes microarray quantitation data to check whether
spotfinding has been done correctly. Spotfinding
EndInfo
}
# user either selects their APES account name, or just a
# range of slide numbers to look at.
sub print_login_page {
print start_form;
#print "";
print h3("Choose a range of slide numbers:");
print p("In this example, pick '5367-5370' " .
"Note that two of these are intentionally " .
"misaligned for demonstration purposes");
print textfield("slide_range");
print p(submit("Find Files"));
print end_form;
}
# choose reference and test files, either those in user's directory
# or in /net/arrays/Quantitation by serial number
sub choose_files {
param("selected_files",""); #This now clears the list
print start_form();
print hidden("slide_range",param("slide_range"));
#print "";
print p("You should check one especially good slide for proper ",
"grid alignment by eye, specify that slide here: ",
"\(For this example, pick 05367.csv as the reference ",
"and the other three for comparison\)");
print popup_menu(
-NAME => "ref_file",
-VALUES => \@quantFiles,
);
print p("Choose the files you want to compare with(for PC uses CTRL-click, ",
"for MAC users APPLE-click):");
print scrolling_list(
-NAME => "selected_files",
-VALUES => \@quantFiles,
-SIZE => 10,
-MULTIPLE => 1,
);
print p(submit("Check")),
end_form;
}
# final page, outputs tables with grid info
sub print_table {
my @quant;
my ( $t0, $t1 );
my @selectedFiles = param("selected_files");
my $refFile = param("ref_file");
unshift @selectedFiles, $refFile;
$t0 = new Benchmark;
for my $n ( 0..$#selectedFiles ) {
readSpotFile( $selectedFiles[$n], \%{$quant[$n]} );
}
$t1 = new Benchmark;
showTimeDiff( $t0, $t1, "read files" );
$t0 = new Benchmark;
findMaxRowCol( \@quant, $#selectedFiles );
$t1 = new Benchmark;
showTimeDiff( $t0, $t1, "find max row & col" );
#print "";
$t0 = new Benchmark;
checkAlign( \@quant, $#selectedFiles, \@selectedFiles, "html" );
$t1 = new Benchmark;
showTimeDiff( $t0, $t1, "check alignment" );
print start_form();
print "";
my $db_name = time;
my $opt = $#selectedFiles - 1; #for now, use opt as 1 less than # slides
my $directory = param("directory");
print end_form;
}
########################
# Subs that do the work
########################
# find files in /net/arrays/Quantitation
sub get_quant_list {
my $slide_range = param("slide_range");
my $low_slide;
my $high_slide;
if($slide_range =~ /\A(\d+)\-(\d+)\Z/) {
$low_slide = $1;
$high_slide = $2;
}
else {
print "ERROR: you must enter a range of numbers!";
exit;
}
my $db_name = time;
for my $i ($low_slide..$high_slide) {
push @quantFiles, glob("../../html/software/GrAPE/grape_demo_files/*$i*");
}
@quantFiles = sort alphanum @quantFiles;
close LIST;
}
# sort ascending alphanumerically
sub alphanum { $a <=> $b }
# html header
sub print_grape_header {
print << "EndHdr"
Middle School Science
