src/hg/utils/phyloTrees/chainNet.pl 1.1

Index: src/hg/utils/phyloTrees/chainNet.pl
===================================================================
RCS file: src/hg/utils/phyloTrees/chainNet.pl
diff -N src/hg/utils/phyloTrees/chainNet.pl
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/utils/phyloTrees/chainNet.pl	9 Dec 2009 18:26:55 -0000	1.1
@@ -0,0 +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
+	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;
+}