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Revision 1.3 - (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 1.2: +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.
#


###########################################
use Carp;
use Data::Dumper;
use FIG_Config;

use FIG;

$dir = "$FIG_Config::global/SimGen";
(! -d $dir) || &FIG::run("rm -rf $dir");
mkdir($dir,0777) || die "could not make $dir";

&FIG::run("make_occ_counts 1.0e-10 | sort +0nr -1 +1 -2 > $FIG_Config::temp/sorted.counts");
&FIG::run("make_protein_sets $FIG_Config::temp/exemplars $FIG_Config::temp/no_hits 1.0e-10 < $FIG_Config::temp/sorted.counts > $FIG_Config::temp/protein.sets");
unlink("$FIG_Config::temp/sorted.counts");
&FIG::run("build_exemplar_fasta < $FIG_Config::temp/exemplars > $dir/exemplar.fasta");
unlink("$FIG_Config::temp/exemplars");
&FIG::run("build_nohit_fasta < $FIG_Config::temp/no_hits > $dir/nohit.fasta");
unlink("$FIG_Config::temp/nohits");
&FIG::run("formatdb -i $dir/nohit.fasta -p T; formatdb -i $dir/exemplar.fasta -p T");
&FIG::run("build_access_sets $dir/AccessSets < $FIG_Config::temp/protein.sets");
unlink("$FIG_Config::temp/protein.sets");

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