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Revision 1.1 - (download) (annotate)
Fri Jul 13 21:25:26 2007 UTC (12 years, 5 months ago) by paczian
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
initial version

#
# 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 strict;
use warnings;

use CGI;
use URI::Escape;
use Data::Dumper;

use FIG;
use FIG_CGI;
use FIG_Config;
use FigWebServices::SeedComponents;
use GenoGraphics;

eval {
    &main;
};

if ($@)
{
    my $cgi = new CGI();

    print $cgi->header();
    print $cgi->start_html();
    
    # print out the error
    print $@;

    print $cgi->end_html();

}

sub main {
    my ($fig, $cgi, $user) = FIG_CGI::init(debug_save   => 0,
                                           debug_load   => 0,
                                           print_params => 0);
    my $peg = $cgi->param('prot') || "fig|83333.1.peg.4";
    my $parameters = { fig_object  => $fig,
		       peg_id      => $peg,
		       table_style => 'plain',
		       fig_disk    => $FIG_Config::fig_disk . "/",
		       form_target => 'region.cgi',
		       title       => "$peg Region",
		       user        => "" };
    
    print $cgi->header();

    print js();

    print FigWebServices::SeedComponents::Framework::get_plain_header($parameters);

    my $gg = get_gg_data($peg, $fig, $cgi);
    foreach (@{&GenoGraphics::render($gg,700,4,0,2)}) {
	print;
    }

    print "</body></html>";

}

sub js {
    my $html_path = "./Html";
    
    return qq~<script src="$html_path\/css\/FIG.js" type="text/javascript"></script>~;
}

sub get_gg_data {
    my ($peg, $fig, $cgi) = @_;

    my $sz_region = 16000;

    my $gg = [];
    my $loc = $fig->feature_location($peg);
    my ($contig,$beg,$end) = $fig->boundaries_of($loc);
    my $all_pegs;
    if ($contig && $beg && $end) {
	my $mid = int(($beg + $end) / 2);
	my $min = int($mid - ($sz_region / 2));
	my $max = int($mid + ($sz_region / 2));
	my $genes = [];
	my ($feat,undef,undef) = $fig->genes_in_region($fig->genome_of($peg),$contig,$min,$max);
	foreach my $fid (@$feat) {
	    my $user = "master";
	    my ($contig1,$beg1,$end1) = $fig->boundaries_of($fig->feature_location($fid));
	    $beg1 = &in_bounds($min,$max,$beg1);
	    $end1 = &in_bounds($min,$max,$end1);
	    my $aliases = join( ', ', $fig->feature_aliases($fid) );
	    my $function = $fig->function_of($fid,$user);
	    my ( $uniprot ) = $aliases =~ /(uni\|[^,]+)/;
	    my $info = join('<br/>', "<b>PEG:</b> $fid",
			    "<b>Contig:</b> $contig1",
			    "<b>Begin:</b> $beg1",
			    "<b>End:</b> $end1",
			    $function ? "<b>Function:</b> $function" : (),
			    $uniprot ? "<b>Uniprot ID:</b> $uniprot" : ()
		);
	    
	    my $sprout = $cgi->param('SPROUT') ? 1 : "";
	    
	    my $fmg = "<a href=\&quot;region.cgi?prot=$fid\&quot>show</a>";
	    
	    my $shape = "Rectangle";
	    if    (($fid !~ /\.bs\./) && ($beg1 < $end1))        { $shape = "rightArrow" }
	    elsif (($fid !~ /\.bs\./) && ($beg1 > $end1))        { $shape = "leftArrow" }
	    
	    push(@$genes,[$fig->min($beg1,$end1),
                          $fig->max($beg1,$end1),
                          $shape,
                          ($fid ne $peg) ? "grey" : 'red',
                          "",
                          $fid,
                          $info, $fmg]);
	    
	    if ($fid =~ /peg/) {
		push(@$all_pegs,$fid);
	    }
	}
	
	#  Sequence title can be replaced by [ title, url, popup_text, menu, popup_title ]
	my $org = $fig->org_of($peg);
	my $desc = "Genome: $org<br />Contig: $contig";
	my $map = [ [ FIG::abbrev( $org ), undef, $desc, undef, 'Contig' ],
		 0,
		 $max+1 - $min,
		 ($beg < $end) ? &decr_coords($genes,$min) : &flip_map($genes,$min,$max)
	    ];
	push(@$gg,$map);
    }
    &GenoGraphics::disambiguate_maps($gg);
    return $gg;
}

sub flip_map {
    my($genes,$min,$max) = @_;
    my($gene);

    foreach $gene (@$genes) {
        ($gene->[0],$gene->[1]) = ($max - $gene->[1],$max - $gene->[0]);
	if      ($gene->[2] eq "rightArrow")  { $gene->[2] = "leftArrow" }
	elsif   ($gene->[2] eq "leftArrow")   { $gene->[2] = "rightArrow" }
    }
    return $genes;
}

sub in_bounds {
    my($min,$max,$x) = @_;

    if     ($x < $min)     { return $min }
    elsif  ($x > $max)     { return $max }
    else                   { return $x   }
}

sub decr_coords {
    my($genes,$min) = @_;
    my($gene);

    foreach $gene (@$genes) {
        $gene->[0] -= $min;
        $gene->[1] -= $min;
    }
    return $genes;
}

sub in {
    my($x,$xL) = @_;
    my($i);

    for ($i=0; ($i < @$xL) && ($x != $xL->[$i]); $i++) {}
    return ($i < @$xL);
}

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