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

#
# 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;
use GenoGraphics;


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

my $html = [];
my $peg = $cgi->param('peg');
if (! $peg)
{
    push(@$html,$cgi->h1("Sorry, but you need to specify a PEG"));
    &HTML::show_page($cgi,$html);
    exit;
}

my @fusions = `$FIG_Config::bin/compute_potential_fusions \'$peg\'`;
if (@fusions < 1)
{
    push(@$html,$cgi->h1("Sorry, no fusions detected"));
    &HTML::show_page($cgi,$html);
    exit;
}

my(@contains,@contained_in);
my($x,$genes,$b,$e,$peg1,$gg);
foreach $_ (@fusions)
{
    chop;
    my($contains,$ln,@parts) = split(/\t/,$_);
    if ($contains eq $peg)
    {
	push(@contains,[@parts]);
	$peg_ln = $ln;
    }
    else
    {
	$key = join(",",map { @f = split(/,/,$_); $f[2] } @parts);
	push(@{$contained_in{$key}}, [$contains,$ln,@parts]);
    }
}

#print &Dumper(["contains",\@contains]);
if (@contains > 0)
{
    push(@$html,$cgi->h1("Given PEG is the Potential Fusion (RED)"));
    if (@contains > 10)
    {
	$_ = @contains;
	push(@$html,$cgi->h1("Truncating from $_ to 10 Cases"));
	$#contains = 9;
    }
	
    $gg = [[&FIG::abbrev($fig->org_of($peg)),1,$peg_ln,[[1,$peg_ln,"rightArrow","red",$peg,&HTML::fid_link($cgi,$peg,0,1)]]]];

    ($x,$genes,$b,$e,$peg1);
    foreach $x (@contains)
    {
	$genes = [];
	foreach $y (@$x)
	{
	    ($b,$e,$peg1) = split(/,/,$y);
	    push(@$genes,[$b,$e,"rightArrow","blue",$peg1,&HTML::fid_link($cgi,$peg1,0,1)]);
	}
	push(@$gg,[&FIG::abbrev($fig->org_of($peg1)),1,$peg_ln,$genes]);
    }
#   print &Dumper(["contains-gg",$gg]);
    push(@$html,@{ &GenoGraphics::render($gg,700,4,0,1) });
    push(@$html,$cgi->hr);
}

#print &Dumper(["contained-in",\%contained_in]);
my(@keys,$key,$contains,@parts);
@keys = keys(%contained_in);
if (@keys > 0)
{
    push(@$html,$cgi->h1("Given PEG (RED) is Potentially Part of a Fusion in Another Genome"));
    foreach $key (@keys)
    {
	$x = $contained_in{$key};
	if (@$x > 10) { $#{$x} = 9 }
	$gg = [];
	foreach $y (@$x)
	{
	    ($contains,$ln,@parts) = @$y;
	    push(@$gg,[&FIG::abbrev($fig->org_of($contains)),1,$ln,[[1,$ln,"rightArrow","blue",$contains,&HTML::fid_link($cgi,$contains,0,1)]]]);
	}
	$genes = [];
	my @just_first = @{$x->[0]};
	splice(@just_first,0,2);
	foreach $part (@just_first)
	{
	    ($b,$e,$peg1) = split(/,/,$part);
	    $color = ($peg1 eq $peg) ? "red" : "green";
	    push(@$genes,[$b,$e,"rightArrow",$color,$peg1,&HTML::fid_link($cgi,$peg1,0,1)]);
	}
	push(@$gg,[&FIG::abbrev($fig->org_of($peg)),1,$x->[0]->[1],$genes]);
#	print STDERR &Dumper($gg);
	push(@$html,@{ &GenoGraphics::render($gg,700,4,0,2) });
	push(@$html,$cgi->hr);
    }
}

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

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