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Revision 1.2 - (download) (annotate)
Sun Apr 27 16:27:13 2008 UTC (11 years, 6 months 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, 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
Changes since 1.1: +5 -2 lines
add line numbers

# -*- 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_anno_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_anno_parms"))
	{
	    print TMP &Dumper($cgi);
	    close(TMP);
	}
    }
    exit;
}


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

my($file);
if (($user = $cgi->param('user')) && ($file = $cgi->param('file')))
{
    &process_file($fig,$cgi,$html,$file,$user);
}
else
{
    push(@$html,$cgi->h1('invalid parameters'));
}

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

sub process_file {
    my($fig,$cgi,$html,$file,$user) = @_;

    if (open(IN,"<$file"))
    {
	my $col_hdrs = ["",'Genome','PEG','Function','Other ID','Their Function'];
	my $tab = [];
	my $N = 1;
	while (defined($_ = <IN>))
	{
	    chomp;
	    my($genome,$peg,$func1,$id,$func2) = split(/\t/,$_);
	    push(@$tab,[$N,
			$fig->genus_species($genome),
			&HTML::fid_link($cgi,$peg),
			$func1,
			&HTML::set_prot_links($cgi,$id),
			$func2]);
	    $N++;
	}
	push(@$html,&HTML::make_table($col_hdrs,$tab,'Annotations to Check'));
    }
    else
    {
	push(@$html,$cgi->h1("could not open $file"));
    }
}


    

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