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Revision 1.6 - (download) (as text) (annotate)
Fri Jun 5 22:59:13 2009 UTC (10 years, 8 months 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_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, 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_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
Changes since 1.5: +1 -0 lines
check for aux roles

# -*- 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 Carp;
use Data::Dumper;

use strict;

use FIG;
my $fig = new FIG;

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

my ( $subsys, $all, $genomes, $role, $pair, $genome, $gs, @pegs, $peg );

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

$genomes = $fig->subsystem_genomes( $subsys, $all );

foreach $role ( $fig->subsystem_to_roles( $subsys ) )
{
    next if ((! $all) && $fig->is_aux_role_in_subsystem($subsys,$role));
    foreach $pair ( @$genomes )
    {
	( $genome, $gs ) = @$pair;
	foreach $peg ( $fig->pegs_in_subsystem_cell( $subsys, $genome, $role ) )
	{
	    print "$role\t$peg\n";
	}
    }
}

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