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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 Assignments;
use strict;

my(%funcs,@poss,@pegs,$func,$peg,$best,@external);

#
# usage: assign_to_sets [-e] < Sets > proposed.assignments
#
# The -e asks that external functions be included.
#

my $parms = &Assignments::load_parms();


while (defined($_ = <STDIN>))
{
    chomp;
    @pegs = split(/\t/,$_);
    if ($ARGV[0] && ($ARGV[0] =~ /^-e/i))
    {
	@external = &external_functions($fig,\@pegs);
    }
    else
    {
	@external = ();
    }

    $best = &Assignments::choose_best_assignment($fig,$parms,\@pegs,\@external);
    if ($best =~ /hypothetical protein/i)
    {
	$best = "hypothetical protein";
    }

    if ($best =~ /^integral membrane protein/i)
    {
	$best = "membrane protein";
    }

    undef %funcs;
    @poss = ();
    my $common = undef;
    my $num_common = 0;
    foreach $peg (@pegs)
    {
	$func = $fig->function_of($peg);
	if (! defined($common))
	{
	    $common = $func;
	    $num_common = 1;
	}
	elsif ($func eq $common)
	{
	    $num_common++;
	}

	if ($best ne $func)
	{
	    my @subs = $fig->peg_to_subsystems($peg);
	    if (@subs == 0)
	    {
		push(@poss,"$peg\t$best\n");
	    }
	    else
	    {
		push(@poss,"CHECK: $peg\t$best\n");
	    }
	}
    }

    if ($num_common < @pegs)
    {
	foreach $_ (@poss)
	{
	    if ($_ =~ /^CHECK/)
	    {
		print STDERR $_;
	    }
	    else
	    {
		print $_;
	    }
	}
    }
}

sub external_functions {
    my($fig,$pegs) = @_;
    my($peg,$alias,%ext);

    foreach $peg (@$pegs)
    {
	foreach $alias (grep { $_ =~ /^(gi\|)|(uni\|)|(sp\|)|(kegg\|)/ } $fig->feature_aliases($peg))
	{
	    $ext{$alias} = 1;
	}
    }
    return keys(%ext);
}


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