d323472f6693dec4cfd0533838563fc6bcdf25f2
hiram
  Fri Aug 9 17:52:50 2019 -0700
xenoRefGene description page fixed up and custom .as definition for the track and correct labelFields on xenoRefGene and ncbiGene refs #23734

diff --git src/hg/utils/automation/doXenoRefGene.pl src/hg/utils/automation/doXenoRefGene.pl
index 41ee395..f5e798d 100755
--- src/hg/utils/automation/doXenoRefGene.pl
+++ src/hg/utils/automation/doXenoRefGene.pl
@@ -263,31 +263,33 @@
 
   my $whatItDoes = "Makes bigGenePred.bb file from filterPsl output.";
   my $bossScript = newBash HgRemoteScript("$runDir/makeGp.bash", $workhorse,
 				      $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export db=$db
 grep NR_ \$db.xenoRefGene.psl > NR.psl
 grep NM_ \$db.xenoRefGene.psl > NM.psl
 mrnaToGene -cdsDb=hgFixed NM.psl NM.gp
 mrnaToGene -noCds NR.psl NR.gp
 cat NM.gp NR.gp | genePredSingleCover stdin \$db.xenoRefGene.gp
 genePredCheck -db=\$db -chromSizes=\$db.chrom.sizes \$db.xenoRefGene.gp
 genePredToBigGenePred -geneNames=$mrnas/geneOrgXref.txt \$db.xenoRefGene.gp \\
    stdout | sort -k1,1 -k2,2n > \$db.bgpInput
-bedToBigBed -extraIndex=name,geneName -type=bed12+8 -tab -as=\$HOME/kent/src/hg/lib/bigGenePred.as \\
+sed -e 's#Alternative/human readable gene name#species of origin of the mRNA#' \\
+  \$HOME/kent/src/hg/lib/bigGenePred.as > xenoRefGene.as
+bedToBigBed -extraIndex=name,geneName -type=bed12+8 -tab -as=xenoRefGene.as \\
    \$db.bgpInput \$db.chrom.sizes \$db.xenoRefGene.bb
 _EOF_
   );
   $bossScript->execute();
 } # doMakeGp
 
 #########################################################################
 # * step: cleanup [workhorse]
 sub doCleanup {
   my $runDir = $buildDir;
 
   if (-e "$runDir/$db.xenoRefGene.gp.gz" ) {
     die "doCleanup: looks like this was run successfully already\n" .
       "($db.xenoRefGene.gp.gz exists).  Investigate the run directory:\n" .
 	" $runDir/\n";