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Revision 1.4 - (download) (as text) (annotate)
Mon Dec 5 18:56:38 2005 UTC (14 years, 7 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 1.3: +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 = "usage: relevant_pchs Genome";

 ($genome = shift @ARGV)
    || die $usage;

if ($genome =~ /^\d+\.\d+$/)
    my $mg = $fig->map_genome_to_id($genome);
    print STDERR "Mapped $genome to $mg\n";
    $genome = $mg;
elsif ($genome =~ /^\d+$/)
    my $g = $fig->map_id_to_genome($genome);
    print STDERR "Using mapped genome $g\n";
    die "Invalid genome identifier\n";

my $qry = 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.g1 = $genome 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 = $dbh->SQL($qry)) && 
    (@$res > 0))
    foreach $x (sort { ($a->[0] <=> $b->[0]) or ($a->[1] <=> $b->[1]) or ($a->[2] <=> $b->[2]) or
			   ($a->[3] <=> $b->[3]) or ($b->[8] <=> $a->[8]) }  @$res)
	print join("\t",@$x),"\n";

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