src/hg/utils/phyloTrees/chainNet.pl 1.2

Index: src/hg/utils/phyloTrees/chainNet.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/phyloTrees/chainNet.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/utils/phyloTrees/chainNet.pl	9 Dec 2009 18:26:55 -0000	1.1
+++ src/hg/utils/phyloTrees/chainNet.pl	9 Dec 2009 18:28:01 -0000	1.2
@@ -1,77 +1,77 @@
 #!/usr/bin/env perl
 # chainNet.pl - output chainNet.ra definitions in phylogentic order
 
 #	$Id$
 
 use strict;
 use warnings;
 use FindBin qw($Bin);
 use lib "$Bin";
 
 my $reroot = "$Bin/rerootTree.pl";
 my $hgsql = "hgsql";
 my $home = $ENV{'HOME'};
 my $dissectTree = "$home/kent/src/hg/utils/phyloTrees/46way.dissect.txt";
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 1) {
     printf STDERR "chainNet.pl - output chainNet.ra definitions in phylogenetic order\n";
     printf STDERR "usage:\n    chainNet.pl <db>\n";
     printf STDERR "<db> - an existing UCSC database\n";
     printf STDERR "will be using commands: rerootTree.pl and hgsql\n";
     printf STDERR "and expecting to find \$HOME/kent/src/hg/utils/phyloTrees/46way.dissect.txt\n";
     printf STDERR "using:\n";
     printf STDERR "$reroot\n";
     printf STDERR "$dissectTree\n";
     exit 255;
 }
 
 my $db = shift;
 my @orderedList;
 my $dbCount = 0;
 my %priorities;
 my $priority = 200.3;
 
 open (FH, "$reroot $db $dissectTree 2> /dev/null|") or die "can not run rerootTree.pl";
 while (my $line = <FH>) {
     chomp $line;
     $orderedList[$dbCount++] = $line;
     $line =~ s/[0-9]+$//;
     if (!exists($priorities{$line})) {
 	$priorities{$line} = $priority;
 	$priority += 10;
     }
 }
 close (FH);
 
 for (my $i = 0; $i < $dbCount; ++$i) {
     my $stripDb = $orderedList[$i];
     $stripDb =~ s/[0-9]+$//;
 #    printf "%02d: %03d %s\n", $i, $priorities{$stripDb}, $orderedList[$i];
 }
 
 my @chainTbls;
 my $chainCount = 0;
 my %orderChainNet;
 
-open (FH, "hgsql -e 'show tables;' $db | grep 'chain.*Link'|") or
+open (FH, "hgsql -e 'show tables;' $db | grep -v -i 'self' | grep 'chain.*Link'|") or
 	die "can not run hgsql 'show tables' on $db";
 while (my $tbl = <FH>) {
     chomp $tbl;
     $tbl =~ s/^chain//;
     $tbl =~ s/Link$//;
     $chainTbls[$chainCount++] = $tbl;
     my $track = "$tbl";
     my $stripDb = $tbl;
     $stripDb =~ s/[0-9]+$//;
     $orderChainNet{$track} = $priorities{lcfirst($stripDb)};
 }
 close (FH);
 
 foreach my $track (sort { $orderChainNet{$a} cmp $orderChainNet{$b} }
 	keys %orderChainNet) {
     my $priority = $orderChainNet{$track};
     printf "track chainNet%s override\n", $track;
     printf "priority %s\n\n", $priority;
 }