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Revision 1.2 - (download) (annotate)
Mon Dec 5 19:12:12 2005 UTC (14 years, 2 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.


=head1 proteininfo.cgi

Get some information about a bunch of proteins. 


#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> ;

  $given = [@inputs];
  $tag_to_id = &parse_inputs($fig,$given); 
  my @ks = keys(%{$tag_to_id});
  $key = $ks[0];
  $key2 = $ks[1]; 
  $values =$tag_to_id->{$key}; 
  $values2 =$tag_to_id->{$key2}; 
  ##print STDERR "valuesof1stkey:@$values[0]\n";
  #print STDERR "valuesof2ndkey:@$values2[0]\n";

if ($tag_to_id && $cgi->param('request') eq "Subsystem Information") 


sub show_initial {
 my ($fig,$cgi,$html)=@_;
 # generate a blank page
 push @$html, 
 "<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",
 "<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>");
  foreach my $h (@headers)
     print STDERR "header:$h\n";
     my $p = $tag_to_id->{$h};
     my @pegs = @$p;
     foreach my $peg (@pegs) 
         print STDERR "peg:$peg\n"; 
         if ($peg =~/(fig\|\d+.\d+.peg.\d+)/){ $peg = $1};
         my @subsystems = $fig->subsystems_for_peg($peg);
         if(@subsystems){print STDERR "OUCH\n"};

         foreach my $ssr (@subsystems)
             $ss = $ssr->[0];
             print STDERR "found ss:$ss\n";
	     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($add){print STDERR "put in all list:$ss\n"; push(@all_subsystems,$ss)}
  my $prefix = &FIG::cgi_url() . "/subsys.cgi?user=&ssa_name=";
  my $suffix = "&request=show_ssa";	
  foreach my $h (@headers)

  foreach my $ss (@all_subsystems)
      print STDERR "each ss: $ss\n";
      my $url = "<a href="."$prefix"."$ss"."$suffix>$ss</a>";	    
      foreach my $h (@headers)
         $key = $ss."_".$h;
         if(!$ss_counter{$key}){$cell = "0"}else{$cell=$ss_counter{$key}}  
   push @$html, &HTML::make_table($table), "\n";
   push(@$html,$cgi->h3("Pegs Not in Subsystem"));
   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>);



=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

sub parse_inputs 

 my ($fig,$given) =@_;
 my $org = pop(@$given);
 my $hash;
 foreach my $g (@$given)
     print STDERR "org:$org\n";
     my $id ="";
     print STDERR "given:$g\n";
     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;
           $id = $temp_id;

		 $list = $hash{$tag};
		 @temp_list = @$list;
		 $hash{$tag} = [@temp_list];
		 @temp_list = ();
		 ##print STDERR "first value for $g:$2\n"; 
                 $hash{$tag} = [@temp_list];
 return \%hash;

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