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Revision 1.5 - (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 1.4: +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.
#


# This is in a highly-unfinished state.  I will work on it more
# once people become available to make their desires known.

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

if (0) {
    my $VAR1;
    eval(join("",`cat /tmp/som_parms`));
    $cgi = $VAR1;
#   print STDERR &Dumper($cgi);
}

if (0) {
    print $cgi->header;
    my @params = $cgi->param;
    print "<pre>\n";
    foreach $_ (@params) {
		print "$_\t:",join(",",$cgi->param($_)),":\n";
    }

    if (0) {
        if (open(TMP,">/tmp/som_parms")) {
	    	print TMP &Dumper($cgi);
	    	close(TMP);
		}
    }
    exit;
}

my $html = [];

my $model = $cgi->param('model');
if ($model && ($model =~ /(\d+\.\d+)/) && ($model = $1) && (-s "$FIG_Config::global/Models/$model"))
{
    &som($fig,$cgi,$html,$model);
}
else
{
    &poss_models($fig,$cgi,$html);
}
&HTML::show_page($cgi,$html);

sub poss_models {
    my($fig,$cgi,$html) = @_;

    my $user = $cgi->param('user');
    if (opendir(MODELS,"$FIG_Config::global/Models") &&
	(@models = grep { ($_ !~ /^\./) && (-s "$FIG_Config::global/Models/$_") } readdir(MODELS)) &&
	(@models > 0))
    {
	my @orgs = sort map { $_ =~ /^(\d+\.\d+)/; 
			      my $org = $1; 
			      my $gs = $fig->genus_species($org); 
			      "$gs ($org)" 
			    } @models;
	push(@$html,$cgi->hr,
	            $cgi->start_form(-action => "status_of_model.cgi"),
	            $cgi->hidden(-name => 'user', -value => $user),
	            $cgi->scrolling_list( -name   => 'model',
					  -values => [ @orgs ],
					  -size   => 10,
					  ), $cgi->br,
	            $cgi->submit('Status of Model'),
	            $cgi->end_form
	     );
    }
    else
    {
	push(@$html,$cgi->h1('Sorry, no PEGs for Models in this SEED'));
    }
}


# I accumulate all the connections and then do nothing
# with them.  I will end up using them, I think

sub som {
    my($fig,$cgi,$html,$model) = @_;
    my(@pegs,$genome,$peg,@in,$tuple,$subsys,$role,@poss,$subsystem,$variant);
    my($reactions,$reaction,%peg2react,%react2peg);

    @pegs = map { ($_ =~ /(fig\|\d+\.\d+\.peg\.\d+)/) ? $1 : () } `cat $FIG_Config::global/Models/$model`;
    if (@pegs < 1) 
    {
	push(@$html,$cgi->h1("Too few PEGs in model for $model"));
    }
    else
    {
	$genome = &FIG::genome_of($pegs[0]);

	foreach $peg (@pegs)
	{
	    @in = $fig->peg_to_roles_in_subsystems($peg);
	    foreach $tuple (@in)
	    {
		($subsys,$role) = @$tuple;
		push(@poss,[$peg,$subsys,$role]);
		$to_check{$subsys}->{$role} = 1;
	    }
	}
    
	foreach $subsys (keys(%to_check))
	{
	    if (($subsystem = new Subsystem($subsys,$fig,0)) &&
		($variant = $subsystem->get_variant_code_for_genome($genome)) &&
		($variant && ($variant ne "-1")))
	    {
		if ($reactions = $subsystem->get_reactions)
		{
		    foreach $role (keys(%{$to_check{$subsys}}))
		    {
			if (($reactions->{$role}))
			{
			    my @pegs = $subsystem->get_pegs_from_cell($genome,$role);
			    foreach $reaction (@{$reactions->{$role}})
			    {
				foreach $peg (@pegs)
				{
				    $peg2react{$peg}->{$reaction} = 1;
				    push(@{$react2peg{$reaction}->{$peg}},[$subsys,$role]);
				}
			    }
			}
		    }
		}
	    }
	}
	&display_connections($fig,$cgi,$html,\@pegs,\%peg2react,\%react2peg);
    }
}

sub display_connections {
    my($fig,$cgi,$html,$pegs,$peg2react,$react2peg) = @_;
    my($peg,$func);

    my $col_hdrs = ["PEG","function","Curator","Subsystem","Role"];
    my $tab = [];
    my $tot = @$peg;

    my $unconnected = 0;

    foreach $peg (sort { &FIG::by_fig_id($a,$b) } @$pegs)
    {
	$tot++;
	if (! $peg2react->{$peg})
	{
	    $unconnected++;
	    $func = $fig->function_of($peg);
	    @in = $fig->peg_to_roles_in_subsystems($peg);
	    if ($tuple = shift @in)
	    {
		($subsys,$role) = @$tuple;
		$cur = $fig->subsystem_curator($subsys);
	    }
	    else
	    {
		$cur = $subsys = $role = "&nbsp;";
	    }
	    push(@$tab,[&HTML::fid_link($cgi,$peg),$func,$cur,$subsys,$role]);

	    foreach $tuple (@in)
	    {
		($subsys,$role) = @$tuple;
		push(@$tab,["","",$fig->subsystem_curator($subsys),$subsys,$role]);
	    }
	}
    }
    push(@$html,&HTML::make_table($col_hdrs,$tab,"PEGs that do not yet connect"));
    $connected = $tot - $unconnected;
    push(@$html,"<hr><b>total PEGs=$tot<br>unconnected=$unconnected<br>connected=$connected<br><hr>");
}
    

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