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Revision 1.1 - (download) (annotate)
Thu Oct 4 04:19:40 2007 UTC (12 years, 1 month ago) by overbeek
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, 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, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
add check_fc.cgi

# -*- 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.
#


use FIG;
my $fig = new FIG;

use Subsystem;

use HTML;
use strict;

use CGI;
my $cgi = new CGI;

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

$fig->set_user($user);

if (0)
{
    my $VAR1;
    eval(join("",`cat /tmp/check_fc_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/check_fc_parms"))
	{
	    print TMP &Dumper($cgi);
	    close(TMP);
	}
    }
    exit;
}

my $html = [];
unshift @$html, "<TITLE>Check FC</TITLE>\n";

my($peg);

if ($peg = $cgi->param('prot'))
{
    my $genome1 = &FIG::genome_of($peg);
    my ($contig,$beg,$end) = $fig->boundaries_of($fig->feature_location($peg));
    my $beg1 = &FIG::max(1,int(($beg+$end)/2) - 5000);
    my $end1 = &FIG::min(int(($beg+$end)/2) + 5000,$fig->contig_ln(&FIG::genome_of($peg),$contig));
    my($features,$beg2,$end2) = $fig->genes_in_region($genome1,$contig,$beg1,$end1);
    my @pegs = grep { ($_ =~ /^fig\|\d+\.\d+\.peg\./) } @$features;

    my(%loc,%similarities);
    foreach my $peg1 (@pegs)
    {
	my($contig1,$b1,$e1) = $fig->boundaries_of($fig->feature_location($peg1));
	$loc{$peg1} = [$contig1,int(($b1+$e1)/2)];
    }

    foreach my $sim ($fig->sims(\@pegs,50000,1.0e-5,"fig"))
    {
	my $id2 = $sim->id2;
	push(@{$similarities{$sim->id1}->{&FIG::genome_of($id2)}},$id2);
	my($contig2,$b2,$e2) = $fig->boundaries_of($fig->feature_location($id2));
	$loc{$id2} = [$contig2,int(($b2+$e2)/2)];
    }
    my %pinned_to;
#
# http://anno-3.nmpdr.org/anno/FIG/chromosomal_clusters.cgi?sim_cutoff=1.0e-5&prot=fig|243274.1.peg.1892&pinned_to=fig|489351.1.peg.3213,fig|266117.1.peg.1288
#
    foreach my $genome (keys(%{$similarities{$peg}}))
    {
	my @pegs1 = @{$similarities{$peg}->{$genome}};
	foreach my $peg2 (grep { $_ ne $peg} @pegs)
	{
	    my $x = $similarities{$peg2}->{$genome};
	    if ($x)
	    {
		my @pegs2 = @$x;
		foreach my $peg1 (@pegs1)
		{
		    my $loc1 = $loc{$peg1};
		    foreach my $peg2 (@pegs2)
		    {
			my $loc2 = $loc{$peg2};
			if (($loc1->[0] eq $loc2->[0]) && (abs($loc1->[1] - $loc2->[1]) < 5000))
			{
			    $pinned_to{$peg1} = 1;
			}
		    }
		}
	    }
	}
    }
    my @pinned_to = keys(%pinned_to);
    my $parm = join(",",@pinned_to);
    $ENV{REQUEST_METHOD} = 'GET';
    $ENV{QUERY_STRING} = "prot=$peg&pinned_to=$parm&sim_cutoff=1.0e-3";
    my $out = join("",`./chromosomal_clusters.cgi`);
    $out =~ s/^.*?(\n<script language)/$1/s;
    $out =~ s/^(.*)\n<hr>.*/$1/s;
    push(@$html,$out);
}
else
{
    push(@$html,$cgi->h1('invalid parameters'));
}

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


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