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Revision 1.4 - (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 1.3: +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;

$usage = "usage: make_assignments_fit_initial_css Prefix RecommenedAssignments Abbr1 Abbr2 ....";

(
 ($prefix = shift @ARGV) &&
 ($assF    = shift @ARGV) && open(ASSF,">$assF")
)
    || die $usage;

%change = map { $_ => 1 } @ARGV;

$/ = "\n//\n";
$_ = <STDIN>;
print $_;

($roles = <STDIN>) || die "bad input file";
chomp $roles;
@roles = map { $_ =~ /^(\S+)\t(\S.*\S)/; [$1,$change{$1} ? "$prefix: $2" : $2] } split(/\n/,$roles);
for ($i=0; ($i < @roles); $i++)
{
    ($abbr,$role) = @{$roles[$i]};
    print "$abbr\t$role\n";
}
print "//\n";

$/ = "\n";

while (defined($_ = <STDIN>) && ($_ !~ /^\/\//))
{
    print $_;
    chop;
    @flds = split(/\t/,$_);
    $genome = $flds[0];

    undef %must_be;
    for ($i=2; ($i < @flds); $i++)
    {
	if ($flds[$i])
	{
	    foreach $peg (split(/,/,$flds[$i]))
	    {
		push(@{$must_be{$peg}},$roles[$i-2]->[1]);
	    }
	}
    }

    foreach $pegN (keys(%must_be))
    {
	$peg = "fig|$genome.peg.$pegN";
	$func  = $fig->function_of($peg);
	@funcs = split(/ [\@\/] |;\s+/,$func);
	@needed = @{$must_be{$pegN}};

	for ($i=0,$ok=1; ($i < @needed) && $ok; $i++)
	{
	    for ($j=0; ($j < @funcs) && ($funcs[$j] ne $needed[$i]); $j++) {}
	    $ok = ($j < @funcs);
	}
	if (! $ok)
	{
	    print ASSF "$peg\t",join(" / ",@needed),"\n";
	}
    }
}
close(ASSF);

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