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Revision 1.3 - (download) (as text) (annotate)
Sat Dec 10 15:10:24 2005 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: +2 -0 lines
minor fixes

#
# 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: make_peg_maps Organisms1 Organisms2 Maps < OldNew.pairs";

(
 ($from = shift @ARGV) &&
 ($to   = shift @ARGV) &&
 ($maps = shift @ARGV)
)
    || die $usage;

&FIG::verify_dir($maps);

my $tmpG = "$FIG_Config::temp/genomes$$";
mkdir("$tmpG",0777) || die "could not make $tmpG";

&FIG::verify_dir("$tmpG/Seqs");
while (defined($_ = <STDIN>))
{
    if ($_ =~ /^(\d+\.\d+)\t(\d+\.\d+)$/)
    {
	$fromO = $1;
	$toO   = $2;

	&FIG::run("cp $from/$fromO/Features/peg/fasta $tmpG/Seqs/$fromO");
	&FIG::run("cp $to/$toO/Features/peg/fasta $tmpG/Seqs/$toO");
	&FIG::run("sims_all p 98 0.7 $tmpG/Seqs $tmpG/Sims $fromO $toO");
	&FIG::run("connections_between $tmpG/Sims 2 1 2> $tmpG/stderr > $tmpG/sets");
	undef %mapping;

	foreach $_ (`cat $tmpG/sets`)
	{
	    if ($_ =~ /^(fig\|(\d+\.\d+)\.peg\.\d+)\t(fig\|(\d+\.\d+)\.peg\.\d+)$/)
	    {
		if (($2 eq $fromO) && ($4 eq $toO))
		{
		    $mapping{$1} = $3;
		}
		elsif (($2 eq $toO) && ($4 eq $fromO))
		{
		    $mapping{$3} = $1;
		}
		else
		{
		    die "INVALID ORGS: $_";
		}
	    }
	}
	open(TMP,">$maps/$fromO-$toO") || die "could not make $maps/$fromO-$toO";
	foreach $_ (sort { $a =~ /(\d+)$\t/; $x = $1; $b =~ /(\d+)\t/; $x <=> $1 } keys(%mapping))
	{
	    print TMP join("\t",($_,$mapping{$_})),"\n";
	}
	close(TMP);
	&FIG::run("rm -r $tmpG/*");
	&FIG::verify_dir("$tmpG/Seqs");
    }
    else
    {
	die "INVALID LINE: $_";
    }
}
system("rm -r $tmpG");

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