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Revision 1.2 - (download) (annotate)
Mon Dec 5 19:12:12 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 1.1: +17 -0 lines
add license words

# -*- perl -*-
#
# 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.
#


=pod

=head1 protein_sets_2.cgi

Get some information about a bunch of proteins. 

=cut

#use strict;
use FIG;
use HTML;
use raelib;
my $raelib=new raelib;
use CGI;
my $cgi=new CGI;
use LWP::Simple qw(!head); # see the caveat in perldoc LWP about importing two head methods.

my $fig;
eval {
    $fig = new FIG;
};  

    
my $html = [];
my $user = $cgi->param('user');

unshift(@$html, "<TITLE>The SEED - Protein Information</TITLE>\n");

my $tag_to_id;
my $inputs;
if ($cgi->param('request') && $cgi->param('korgs') ) 
{
  my $input =$cgi->param('proteins');
  my @inputs = split("\n",$input);
  push @orgs, $cgi->param('korgs');
  $org = $orgs[0];

  if ($cgi->upload('fileupload'))
  {
     my $fh=$cgi->upload('fileupload');
     @inputs = <$fh> ;
  }

  push(@inputs,$org);
  $given = [@inputs];
  $tag_to_id = &parse_inputs($fig,$given); 
 
}

if ($tag_to_id && $cgi->param('request') eq "Subsystem Information") 
{
    &subsystem_info($fig,$cgi,$html,$tag_to_id);
}
else
{
 
  &show_initial($fig,$cgi,$html);
  &HTML::show_page($cgi,$html,1);
  exit;

}



sub show_initial {
 my ($fig,$cgi,$html)=@_;
 # generate a blank page
 push @$html, 
 $cgi->start_multipart_form(),
 "<p>Select an Organism from the list.\n Enter list of tag and id pairs where the tag represents an expression level in a  microarray experiment or an isolate from a complete genome hybridization experiment and the id is a gene/protein id or alias</p>\n",
 "<p>",
 "<br><b>Choose one or more organisms from this list:</b><br>\n",
 $raelib->scrolling_org_list($cgi, "1"),
 
 "<b>Paste tag ID pairs here:</b><br>\n",
 $cgi->textarea(-name=>"proteins", -rows=>10, -columns=>40), "<br>\n", 
 "<br><b>Or choose a file here:</b><br>\n",
 $cgi->filefield(-name=>"fileupload", -size=>50), "<br>\n",
 $cgi->submit(-name=>'request', -value=>'Subsystem Information'), 
 $cgi->submit(-name=>'request', -value=>'Paint Subsystem Network Diagram'), 
 $cgi->reset, $cgi->end_form;
 return $html;
}

sub subsystem_info 
{
  my ($fig,$cgi,$html,$tag_to_id)=@_;
  
  my $html = [];
  my $table = [];
  my @headers = keys(%{$tag_to_id});
  my $ss_counter;
  my @all_subsystems;
  my @pegs_with_no_ss;

  push (@$html,"<br><br>");
  my $first_header = 1;
  my $pegs_to_color_suffix;
  foreach my $h (@headers)
  {
     my $p = $tag_to_id->{$h};
     my @pegs = @$p;
     foreach my $peg (@pegs) 
     {
         if($first_header){$pegs_to_color_suffix = $pegs_to_color_suffix."&color=$peg"}
         if ($peg =~/(fig\|\d+.\d+.peg.\d+)/){ $peg = $1};
         my @subsystems = $fig->subsystems_for_peg($peg);

         if(!$subsystems[0]){push(@pegs_with_no_ss,$peg)};
         foreach my $ssr (@subsystems)
         {
             $ss = $ssr->[0];
	     my $key = $ss."_".$h;
             if($ss_counter{$key}){$ss_counter{$key} = $ss_counter{$key} + 1}
             else{$ss_counter{$key} = 1}
             my $add = 1;
             foreach my $s (@all_subsystems){if($s eq $ss){$add= 0}}
             if($add){push(@all_subsystems,$ss)}
         }
     }
     $first_header = 0;
  }
 
  my $prefix = &FIG::cgi_url() . "/display_subsys.cgi?user=&ssa_name=";
  my $suffix = "&request=show_ssa".$pegs_to_color_suffix;	
  push(@$table,"<TABLE><TR><TH>Subsystems</TH>");
  foreach my $h (@headers)
  {
      push(@$table,"<TH>\t$h\t</TH>");
  }
  push(@$table,"</TR>");

  foreach my $ss (@all_subsystems)
  {
      my $url = "<a href="."$prefix"."$ss"."$suffix>$ss</a>";	    
      push(@$table,"<TR><TD>$url</TD>");
      foreach my $h (@headers)
      {
         $key = $ss."_".$h;
         if(!$ss_counter{$key}){$cell = "0"}else{$cell=$ss_counter{$key}}  
     	 push(@$table,"<TD>$cell</TD>");
      }
      push(@$table,"</TR>");
        
   }     
         
   push(@$table,"</TABLE>");
   push @$html, &HTML::make_table($table), "\n";
         
   push(@$html,$cgi->h3("Pegs Not in Subsystem"));
   push(@$html,"<TABLE>");
	
   foreach my $p (@pegs_with_no_ss)
   {
        my $cgi = &FIG::cgi_url();
	my $url =qq(<a href="$cgi/protein.cgi?prot=$p&user=">$p</a>);
	push(@$html,"<TR><TD>$url</TD></TR>");
   }
	 
   push(@$html,"</TABLE>");

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

}

=head2 parse_inputs

Given a list of of tab-separated tags and protein ids
return a hash with the tag as key and the value is a list of values
=cut

sub parse_inputs 
{

 my ($fig,$given) =@_;
 my $org = pop(@$given);
 my $hash;
  
 foreach my $g (@$given)
 {
     my $id ="";
     if ($g =~/(\w+)\s+(.*)/)
     {
         $tag = $1;
         $temp_id = $2;

         if($temp_id !~/fig/)
         { 
	     ($peg_index_data,undef) = $fig->search_index($temp_id);
             foreach $peg (map { $_->[0] } @$peg_index_data)
             {
		 if ($peg  =~ /$org/ )
		 {  
		     $id = $peg;
	         }
             }
         }
         else
         {
           $id = $temp_id;
         }

         if($id)
         { 
	     if($hash{$tag})
	     {
		 $list = $hash{$tag};
		 @temp_list = @$list;
		 push(@temp_list,$id);
		 $hash{$tag} = [@temp_list];
	     }
	     else
	     {
		 @temp_list = ();
		 push(@temp_list,$id);
                 $hash{$tag} = [@temp_list];
             }
         } 
     }
 }
 
 return \%hash;
}
 

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