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Revision 1.7 - (download) (as text) (annotate)
Mon Sep 4 20:21:31 2006 UTC (13 years, 2 months ago) by redwards
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
Changes since 1.6: +1 -1 lines
using is_environmental instead of seven 9s

#
# 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;

$usage = "usage: extend_subsys HtmlDIR Subsystem User";

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

(-d $html_dir) || mkdir($html_dir,0777) || die "could not mkdir $html_dir";

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 %in = map { $_ => 1 } grep { &ok_variant($variant_codes{$_}) } @genomes;
my @out = grep { ! $in{$_} } grep { !$fig->is_environmental($_) } $fig->genomes("complete");

foreach $genome (@out)
{
    $known_hits{$genome} = &known_hits($fig,$genome,\@roles);
}
@out = sort { ($known_hits{$b} <=> $known_hits{$a}) or ($a cmp $b) } @out;

foreach $genome (@out)
{
    next if (-s "$html_dir/$subsys.$genome.html");
    print STDERR "processing $genome\n";
    $ENV{"REQUEST_METHOD"} = "GET";
    $ENV{"QUERY_STRING"}   = "subsystem=$subsys&genome=$genome&request=extend_ssa_with_genome&user=$user";
    @html = `$FIG_Config::fig_disk/FIG/CGI/extend_subsys.cgi`;

    while ((@html > 0) && ($html[0] !~ /\<html\>/i))
    {
	shift @html;
    }
    if (@html > 0)
    {
	if (open(HTML,">$html_dir/$subsys.$genome.html"))
	{
	    print HTML join("",@html);
	    close(HTML);
	}
    }
}

sub known_hits {
    my($fig,$genome,$roles) = @_;
    my($role,$hits);

    $hits = 0;
    foreach $role (@$roles)
    {
	if (my @tmp1 = $fig->seqs_with_role($role,"master",$genome))
	{
	    $hits++;
	}
    }
    return $hits;
}

sub ok_variant {
    my($variant) = @_;

    return ($variant && ($variant ne "-1"));
}


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