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Revision 1.5 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 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.

#
# 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;

$usage = "usage: fill_subsys Subsystem User";

(
 ($subsys   = shift @ARGV) &&
 ($user     = shift @ARGV)
)
    || die $usage;

$cgi->param(-name => 'user', -value => $user);

my $sub     = $fig->get_subsystem($subsys);
$sub || (die "$subys does not exist on this machine");

my @roles   = $sub->get_roles;
my @genomes       = $sub->get_genomes;
my %variant_codes = map { $_ => $sub->get_variant_code($sub->get_genome_index($_)) } @genomes;
my @roles         = $sub->get_roles;

my $html = [];
my($genome);

foreach $role (@roles)
{
    foreach $genome (@genomes)
    {
	push(@{$known{$role}},$sub->get_pegs_from_cell($genome,$role));
    }
}
# print STDERR &Dumper(\%known);

my $col_hdrs = ["Candidate","Length","Current Function","In Sub", "Score","Matched","Length","Function","UniProt Function"];

foreach $genome (@genomes)
{
    my @html = ();
    my $gs = $fig->genus_species($genome);

    foreach $role (@roles)
    {
	$known = $known{$role};
	if (@$known > 0)
	{
#	    print STDERR "Filling $genome: $role\n";

	    @tmp = $sub->get_pegs_from_cell($genome,$role);
	    if (@tmp == 0)
	    {
		my @hits = $fig->best_bbh_candidates($genome,1.0e-20,10,$known);
		@candidates = sort { $a->[2] <=> $b->[2] } @hits;

		if (@candidates > 0)
		{
		    my $tab = [];
		    foreach $tuple (@candidates)
		    {
			my($my_peg,$match_peg,$psc) = @$tuple;
#			print STDERR &Dumper(["tuple=",$tuple,$match_peg,$psc]);
			my $my_peg_link = &HTML::fid_link($cgi, $my_peg, 1);
			my $match_peg_link = &HTML::fid_link($cgi, $match_peg, 0);
			my $my_len    = $fig->translation_length($my_peg);
			my $match_len = $fig->translation_length($match_peg);
			my $my_fn     = $fig->function_of($my_peg);
			my $match_fn  = $fig->function_of($match_peg);
			my @in_sub    = $fig->peg_to_subsystems($my_peg);
			my $in_sub    = (@in_sub > 0) ? @in_sub : "&nbsp;";
			my $uni = $fig->to_alias($my_peg,"uni");
			my $uni_func = $uni ? $fig->function_of($uni) : "";
			push(@$tab, [$my_peg_link, $my_len, $my_fn,$in_sub,
				     $psc,
				     $match_peg_link, $match_len, $match_fn,$uni_func]);
		    }

		    push(@html, &HTML::make_table($col_hdrs, $tab, "Candidates for $role"),
			 $cgi->br,$cgi->br
		        );
		    
		}
	    }
	}
    }
    
    if (@html > 0)
    {
	push(@$html,$cgi->h1("Expansion for $genome: $gs"));
	push(@$html,@html);
	push(@$html,$cgi->hr);
    }
}

if (@$html == 0)
{
    push(@$html,$cgi->h1('Sorry, could be filled in'));
}

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

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