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Revision 1.3 - (download) (as text) (annotate)
Sat Jan 7 23:11:10 2006 UTC (14 years, 2 months ago) by overbeek
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: +1 -1 lines
fixes to salvage code

########################################################################
#
# 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;

my $usage = "usage: salvage_master_annotations OldData NewData Maps OldNewMap";

(
 ($oldData = shift @ARGV) &&
 ($newData = shift @ARGV) &&
 ($maps    = shift @ARGV) &&
 ($old_new = shift @ARGV)
)
    || die $usage;

my $oldOrg = "$oldData/Organisms";
my $newOrg = "$newData/Organisms";

if (! -d $maps)
{
    &run("make_peg_maps $oldOrg $newOrg $maps < $old_new");
}

opendir(NEW,"$newOrg") || die "could not open $newOrg";
foreach my $org (grep { $_ =~ /^\d+\.\d+$/ } readdir(NEW))
{
    if (-d "$oldOrg/$org")
    {
	if (-s "$oldOrg/$org/assigned_functions")
	{
	    system("cp", "$oldOrg/$org/assigned_functions","$newOrg/$org/assigned_functions");
	}

	if (-s "$oldOrg/$org/annotations")
	{
	    system("cp", "$oldOrg/$org/annotations","$newOrg/$org/annotations");
	}
    }
}

foreach $_ (`cat $old_new`)
{
    if ($_ =~ /^(\d+\.\d+)\t(\d+\.\d+)$/)
    {
	$old = $1;
	$new = $2;
	if ((-d "$oldOrg/$old") && (-d "$newOrg/$new") && (-s "$maps/$old-$new"))
	{
	    print STDERR "making assignments for $new from $old\n";
	    &FIG::run("salvage_annotations $oldOrg/$old $newOrg/$new $maps/$old-$new");
	}
	else
	{
	    print STDERR "bad input pair: $_";
	}
    }
}
system "rm -r $newData/Subsystems/*"   # clear out subsystems to pull in from master
&FIG::run("salvage_subsystem_rows $oldData/Subsystems $newData/Subsystems $maps $newData");
&FIG::run("index_annotations");
&FIG::run("index_subsystems");
&FIG::run("add_assertions_of_function");


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