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Revision 1.8 - (download) (as text) (annotate)
Fri Oct 23 22:14:03 2009 UTC (10 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, 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, rast_rel_2011_0119, 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, mgrast_dev_04012011, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
Changes since 1.7: +1 -1 lines
fix documentation

# -*- 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;
$fig = new FIG;

my $usage = "usage: pegs_in_subsystems [ all ] > SUBSYS-ROLE-PEG\nThe 'all' parameter is required to include genomes without an operational variant\n\n";

my $all = ((@ARGV > 0) && ($ARGV[0] =~ /^all/i));

foreach $subsys (grep { $fig->usable_subsystem($_) } $fig->all_subsystems)
{
    @roles    = $fig->subsystem_to_roles($subsys);
    if (! $all)
    {
	@roles = grep { ! $fig->is_aux_role_in_subsystem($subsys,$_) } @roles;
    }

    $genomes  = $fig->subsystem_genomes($subsys,$all);
    foreach $role (@roles)
    {
	foreach $pair (@$genomes)
	{
	    ($genome,$gs) = @$pair;
	    @pegs = $fig->pegs_in_subsystem_cell($subsys,$genome,$role);
	    foreach $peg (@pegs)
	    {
		print "$subsys\t$role\t$peg\n";
	    }
	}
    }
}

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