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Revision 1.14 - (download) (annotate)
Mon Dec 5 19:12:11 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, caBIG-05Apr06-00, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.13: +17 -0 lines
add license words

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

use FIG;
my $fig = new FIG;
use HTML;
use CGI;

my $cgi = new CGI;
my $html = [];
my @pegs_with_no_ss = ();

if($cgi->param('genome') && $cgi->param('attribute') && $cgi->param('value'))
{
        
        push (@$html, "<TITLE>Connect Differentially Expressed Pegs to Subsystems</TITLE>");
	push(@$html, $cgi->br,$cgi->hr);	
        push(@$html,$cgi->h3("Subsystems: # of pegs with matching expression level"));
 	my $genome_string = $cgi->param('genome');
	my @string_parts = split(", ",$genome_string);
        my $genome = $string_parts[1]; 
	my $att_param = $cgi->param('attribute');
	my $value_param = $cgi->param('value');
       	my $ss_counter;
        my @all = $fig->all_subsystems();
	foreach my $a (@all){ $ss_counter{$a} = 0 } 
	my @pegs = $fig->pegs_of($genome);
        my %list_of_ss; 
 	foreach my $peg (@pegs) {
                next unless (my @attr=$fig->get_attributes($peg));
                foreach my $attr (@attr) {
   			next unless (defined $attr);
        		my ($gotpeg, $tag, $val, $link)=@$attr;
	        	next unless ($tag eq $att_param);
                       	next unless($val eq $value_param);
			my @subsystems = $fig->subsystems_for_peg($peg);
			my $no_ss = 1;
                        foreach my $ss (@subsystems)
			{  
                                my $ss_name = $ss->[0];
				$counter = $ss_counter{$ss_name};
				$counter = $counter + 1;
                 		$list_of_ss{$ss_name} = "1";
                                $ss_counter{$ss_name} = $counter; 
				$no_ss = 0;
                	}
			if($no_ss){push(@pegs_with_no_ss,$peg)}
                 }
        } 
        my @list = keys(%list_of_ss);
	
	my $prefix = subsys.cgi?user=&ssa_name=";
	my $suffix = "&request=show_ssa";	
        push(@$html,"<TABLE>");
        foreach my $s (@list)
	{
           my $peg_count = $ss_counter{$s};
	   my $url = "<a href="."$prefix"."$s"."$suffix"."&color_by_peg_tag=$att_param".">$s</a>";	    
	   push(@$html,"<TR><TD>$url</TD><TD>$peg_count</TD></TR>");
     	     
         }
         push(@$html,"</TABLE>",$cgi->hr);
         
         push(@$html,$cgi->h3("Pegs Not in Subsystem"));
 	 push(@$html,"<TABLE>");
	
	 foreach my $p (@pegs_with_no_ss)
	 {
		my $cgi = &FIG::cgi_url(-relative => 1);
		my $url =qq(<a href="protein.cgi?prot=$p&user=">$p</a>);
	   	push(@$html,"<TR><TD>$url</TD></TR>");
	 }
	 push(@$html,"</TABLE>");

         &HTML::show_page($cgi,$html);
}
 
else{ 

	$html = [];
	push @$html, "<TITLE>Connect Differentially Expressed Pegs to Subsystems</TITLE>";

	push(@$html,$cgi->start_form(-action => "array2sub.cgi",  -method => 'post'));


	my @gs_list;
	my @genomes = $fig->genomes('complete');
	foreach $g (@genomes){
		my $gs = $fig->genus_species($g);
		push(@gs_list, $gs.", ".$g);
	}

	@gs_list2 =sort {uc($a) cmp uc($b)} @gs_list;
	push(@$html,
     		$cgi->h3("select genome"),
     		$cgi->scrolling_list(-name => 'genome',
			  -values => [@gs_list2],
			  -size => 10,
			   -multiple => 1
			  ),
    		$cgi->hr
	);

	#my $opt=$fig->get_keys("peg"); # all the peg tags
	#my @options=sort {uc($a) cmp uc($b)} keys %$opt;
	#unshift(@options, undef); 
	@options =("microarray_sigmaB_regulon","pH_75_vs_55");
	push(@$html,$cgi->h3("select experiment"), $cgi->popup_menu(-name => 'attribute', -values=>\@options), $cgi->br, $cgi->hr);

	@options2 = ("up regulated","down regulated","present");
	push(@$html,$cgi->h3("select value"), $cgi->popup_menu(-name => 'value', -values=>\@options2), $cgi->br,$cgi->hr);

	push(@$html,$cgi->submit('find subsystems'), $cgi->end_form);

	&HTML::show_page($cgi,$html);

}

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