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Revision 1.8 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 2 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 1.7: +17 -0 lines
Add license words.

# -*- 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.
#

#
# You must build the FIG/Data/NR directory to reflect the set of external
# sources you wish integrated into the SEED
#

use FIG;

&shutdown_browser;

$scr = "$FIG_Config::temp/NR.update.$$";
mkdir($scr,0777) || die "could not make $scr";

&FIG::run("cat $FIG_Config::data/NR/*/assigned_functions > $FIG_Config::global/ext_func.table");
&FIG::run("cat $FIG_Config::data/NR/*/org.table  > $FIG_Config::global/ext_org.table");
&FIG::run("load_external_orgs");
&FIG::run("add_assertions_of_function");

&FIG::run("build_nr_sources > $scr/nr.sources");
&FIG::run("build_nr $scr/nr.sources $scr/nr $scr/peg.synonyms");
&FIG::run("compute_changed_ids_for_nrs $FIG_Config::global/nr $FIG_Config::global/peg.synonyms $scr/nr $scr/added.ids $scr/deleted.ids $scr/replaced.ids");
&FIG::run("pull_fasta_entries $scr/nr < $scr/added.ids > $scr/fasta.added.entries");
&FIG::run("process_sim_deletions_and_replacements $FIG_Config::data/Sims $scr/Sims $scr/replaced.ids $scr/deleted.ids");
mkdir("$scr/NewSims",0777) || die "could not make $scr/NewSims";

print STDERR "Now build similarities from 

          $scr/peg.synonyms
          $scr/fasta.added.entries
          $scr/nr

and then put the new similarities into

          $scr/NewSims

and run

          import_external_sequences_step3 $scr

";

sub shutdown_browser {

    open(WHY,">$FIG_Config::global/why_down") 
	|| die "could not open why_down";
    print WHY "The system is inaccessable due to an update of external sequences; this may take a bit";
    close(WHY);
}


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