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Revision 1.3 - (download) (as text) (annotate)
Mon Dec 5 18:56:38 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 1.2: +17 -0 lines
Add license words.

# 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;

use DBrtns;
my $dbh = $fig->db_handle;

# usage: relevant_PCHs < PEGs > PCHs

while (defined($peg = <STDIN>))
    chomp $peg;

    my @mapped = $fig->map_peg_to_ids($peg);

    my($gnum, $pnum) = @mapped;

    $gnum =~ /\d+/ or die "Could not map peg $peg\n";

    my $res = $dbh->SQL(qq(SELECT r1.g1, r1.p1,
			   r1.g2, r1.p2,
			   r2.g2, r2.p2,
			   r3.g2, r3.p2,
			   r2.iden, r3.iden, r2.paraN, r3.paraN

                           FROM close_pegs r1, condensed_sims r2, condensed_sims r3, close_pegs r4
                           WHERE (r1.p1 = $pnum AND
				  r1.g1 = $gnum AND
				  r1.g1 = r2.g1 AND
				  r1.p1 = r2.p1 AND
				  r1.g2 = r3.g1 AND
				  r1.p2 = r3.p1 AND
				  r4.g1 = r2.g2 AND
				  r4.p1 = r2.p2 AND
				  r4.g2 = r3.g2 AND
				  r4.p2 = r3.p2)

    if ($res)
	foreach $x (@$res)
	    print join("\t",@$x),"\n";

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