src/hg/utils/phyloTrees/chainNet.pl 1.5

Index: src/hg/utils/phyloTrees/chainNet.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/phyloTrees/chainNet.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/utils/phyloTrees/chainNet.pl	22 Jan 2010 18:40:22 -0000	1.4
+++ src/hg/utils/phyloTrees/chainNet.pl	1 Apr 2010 17:04:12 -0000	1.5
@@ -1,115 +1,117 @@
 #!/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";
 
 # new genomes since the 46-way construction.  This will keep
 #	the priority numbers the same for the previous 46 and place
 #	these new ones in between the previous ones.
-my $newAssemblies = "ailMel susScr";
+my $newAssemblies = "ailMel susScr oviAra";
 my $newAssemblyOffset = 5;
 my $offset46way = 10;
 my $reroot = "$Bin/rerootTree.pl";
 my $hgsql = "hgsql";
 my $home = $ENV{'HOME'};
-my $dissectTree = "$home/kent/src/hg/utils/phyloTrees/48way.dissect.txt";
+my $dissectTree = "$home/kent/src/hg/utils/phyloTrees/49way.dissect.txt";
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 1) {
     printf STDERR "chainNet.pl - output chainNet.ra definitions in phylogenetic order\n";
     printf STDERR "usage:\n    chainNet.pl <db>\n";
     printf STDERR "<db> - an existing UCSC database\n";
     printf STDERR "will be using commands: rerootTree.pl and hgsql\n";
-    printf STDERR "and expecting to find \$HOME/kent/src/hg/utils/phyloTrees/48way.dissect.txt\n";
+    printf STDERR "and expecting to find \$HOME/kent/src/hg/utils/phyloTrees/49way.dissect.txt\n";
     printf STDERR "using:\n";
     printf STDERR "$reroot\n";
     printf STDERR "$dissectTree\n";
     exit 255;
 }
 
 my $initialPrio = 200.3;
 my $db = shift;
 my $dbCount = 0;
 my %priorities;
 my $priority = $initialPrio;
 my $stripName = $db;
 $stripName =~ s/[0-9]+$//;
 
 my $actualTreeName = "notFound";
 
 # given an arbitrary database name, find corresponding database name
 # that is actually in the phylo tree
 open (FH, "grep name $dissectTree | sort -u | sed -e \"s/.*name = '//; s/'.*//;\"|") or die "can not read $dissectTree";
 while (my $name = <FH>) {
     chomp $name;
     my $treeName = $name;
     $name =~ s/[0-9]+$//;
     if ($name eq $stripName) {
 	$actualTreeName = $treeName;
 	last;
     }
 }
 
 # verify we found one
 if ($actualTreeName eq "notFound") {
     printf "ERROR: specified db '$db' is not like one of the databases in the phylo tree\n";
     printf `grep name $dissectTree | sort -u | sed -e "s/.*name = '//; s/'.*//;" | xargs echo`, "\n";
     exit 255;
 }
 
 # reroot the tree to that database name
 open (FH, "$reroot $actualTreeName $dissectTree 2> /dev/null|") or die "can not run rerootTree.pl";
 while (my $line = <FH>) {
     chomp $line;
     $line =~ s/[0-9]+$//;
     if (!exists($priorities{lcfirst($line)})) {
 	if ($newAssemblies =~ m/$line/) {
 	    $priority -= $newAssemblyOffset;
 	    $priorities{lcfirst($line)} = $priority;
 	    $priority += $newAssemblyOffset;
 	} else {
 	    $priorities{lcfirst($line)} = $priority;
 	    $priority += $offset46way;
         }
     }
 }
 close (FH);
 
 my $chainCount = 0;
 my %orderChainNet;
 
 # fetch all chain tables from the given database and for ones that are
 # in the phylo tree, output their priority
 open (FH, "hgsql -e 'show tables;' $db | grep 'chain.*Link' | egrep -i -v 'self|chainNet' | sed -e 's/^.*_chain/chain/' | sort -u|") or
 	die "can not run hgsql 'show tables' on $db";
 while (my $tbl = <FH>) {
     chomp $tbl;
     $tbl =~ s/^chain//;
     $tbl =~ s/Link$//;
     my $track = $tbl;
     my $stripDb = $tbl;
     $stripDb =~ s/[0-9]+$//;
+    $stripDb =~ s/V17e$//;
+    $stripDb =~ s/Poodle$//;
     if (defined($stripDb) && length($stripDb) > 0) {
 	if (exists($priorities{lcfirst($stripDb)})) {
 	    my $priority = $priorities{lcfirst($stripDb)};
 	    $orderChainNet{$track} = $priority;
 	} else {
-	    printf STDERR "warning: not in phylo tree: $tbl\n";
+	    printf STDERR "warning: not in phylo tree: $tbl ($stripDb)\n";
 	}
     }
 }
 close (FH);
 
 # print out the priorities in order by priority, lowest first
-foreach my $track (sort { $orderChainNet{$a} cmp $orderChainNet{$b} }
+foreach my $track (sort { $orderChainNet{$a} <=> $orderChainNet{$b} }
 	keys %orderChainNet) {
     my $priority = $orderChainNet{$track};
     printf "track chainNet%s override\n", $track;
     printf "priority %s\n\n", $priority;
 }