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Revision 1.3 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 4 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 1.2: +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.
#


$usage = "usage: make_fig_files TrustedSubsystems Fasta Id.map FamFunc";

(
 ($subsystems = shift @ARGV) && (-s $subsystems) &&
 ($fasta      = shift @ARGV) && open(FASTA,">$fasta") &&
 ($id_map     = shift @ARGV) && open(IDMAP,">$id_map") &&
 ($fam_func   = shift @ARGV) && open(FAMFUNC,">$fam_func")
)
    || die $usage;

use FIG;
my $fig = new FIG;

@sub = map { ($_ =~ /(\S[^\t]*\S)/) ? $1 : () } `cat $subsystems`;

my %in__role;
foreach $sub (@sub)
{
    print STDERR "$sub\n";
    @genomes = map { $_->[0] } @{$fig->subsystem_genomes($sub)};
    @roles = $fig->subsystem_to_roles($sub);
    foreach $role (@roles)
    {
	print STDERR "  $role\n";
	foreach $genome (@genomes)
	{
            @pegs = $fig->pegs_in_subsystem_cell($sub,$genome,$role);
	    foreach $peg (@pegs)
	    {
		$in_role{$role}->{$peg} = 1;
	    }
	}
    }
}

$fam = "000001";
foreach $role (keys(%in_role))
{
    my $hash = $in_role{$role};
    foreach $peg (keys(%$hash))
    {
	if ($seq = $fig->get_translation($peg))
	{
	    print IDMAP "fig|PF$fam\t$peg\n";
	    print FASTA ">$peg\n$seq\n";
	}
    }

    print FAMFUNC "fig|PF$fam\t$role\n";
    $fam++;
}

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