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Revision 1.6 - (download) (as text) (annotate)
Thu Jan 26 13:40:11 2006 UTC (13 years, 9 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 1.5: +1 -0 lines
load ext org table on update_nr_cycle

########################################################################
# -*- 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 strict;
use FIG;
my $fig = new FIG;

if (! &verify_NR)
{
    print STDERR "Exiting, since you have a messed up NR directory\n";
    exit;
}

my $tmp_sources = "$FIG_Config::temp/nr.sources.$$";
my $tmp_nr      = "$FIG_Config::temp/nr.$$";
my $tmp_syn     = "$FIG_Config::temp/peg.synonyms.$$";
my $tmp_added   = "$FIG_Config::temp/added.$$";
my $tmp_changed = "$FIG_Config::temp/changed.$$";
my $tmp_deleted = "$FIG_Config::temp/deleted.$$";

&FIG::run("build_nr_sources > $tmp_sources");
&FIG::run("build_nr $tmp_sources $FIG_Config::global/nr $FIG_Config::global/peg.synonyms $tmp_nr $tmp_syn");
&FIG::run("echo \"Brought SEED down to update NR; back as quickly as possible\" > $FIG_Config::global/why_down");
&FIG::run("compute_changed_ids_for_nrs $FIG_Config::global/nr $FIG_Config::global/peg.synonyms $tmp_nr $tmp_added $tmp_changed $tmp_deleted");
# if (-s $tmp_deleted)   { die "Something got deleted" }  ### it's ok to delete and not reclaim
# if (-s $tmp_changed)   { die "Something got changed" }
my @ids = map { $_ =~ /^(\S+)/; $1 } `cat $tmp_added`;
$fig->enqueue_similarities(\@ids);

rename("$FIG_Config::global/nr","$FIG_Config::global/nr~");
rename("$FIG_Config::global/peg.synonyms","$FIG_Config::global/peg.synonyms~");
&FIG::run("cp $tmp_nr $FIG_Config::global/nr");
&FIG::run("cp $tmp_syn $FIG_Config::global/peg.synonyms");
&FIG::run("load_peg_mapping");
&FIG::run("load_features");   #### needed to pick up aliases from the updated peg.synonymns
&FIG::run("cat $FIG_Config::data/NR/*/org.table > $FIG_Config::global/ext_org.table");
&FIG::run("cat $FIG_Config::data/NR/*/assigned_functions > $FIG_Config::global/ext_func.table");
&FIG::run("load_external_orgs");
&FIG::run("add_assertions_of_function");
&FIG::run("make_indexes");
unlink("$FIG_Config::global/why_down");
unlink($tmp_sources,$tmp_nr,$tmp_syn,$tmp_added,$tmp_deleted,$tmp_changed);

sub verify_NR {

    if (opendir(NR,"$FIG_Config::data/NR"))
    {
	my @sources = grep { $_ !~ /^\./ } readdir(NR);
	closedir(NR);
	foreach my $source (@sources)
	{
	    if (! ((-s "$FIG_Config::data/NR/$source/fasta") &&
		   (-s "$FIG_Config::data/NR/$source/assigned_functions") &&
		   (-s "$FIG_Config::data/NR/$source/org.table")))
	    {
		return 0;
	    }
	}
	return 1;
    }
    return 0;
}

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