7a5cff1bced06596181624623f86a803c4be59f6
hiram
  Mon Aug 12 14:00:53 2019 -0700
correct searching enabled on xenoRefGene track refs #23734

diff --git src/hg/utils/automation/doXenoRefGene.pl src/hg/utils/automation/doXenoRefGene.pl
index f5e798d..be16b2f 100755
--- src/hg/utils/automation/doXenoRefGene.pl
+++ src/hg/utils/automation/doXenoRefGene.pl
@@ -263,63 +263,66 @@
 
   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
-sed -e 's#Alternative/human readable gene name#species of origin of the mRNA#' \\
+sed -e 's#Alternative/human readable gene name#species of origin of the mRNA#; s#Name or ID of item, ideally both human readable and unique#RefSeq accession id#; s#Primary identifier for gene#gene name#;' \\
   \$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
+\$HOME/kent/src/hg/utils/automation/xenoRefGeneIx.pl \$db.bgpInput | sort -u > \$db.ix.txt
+ixIxx \$db.ix.txt \$db.xenoRefGene.ix \$db.xenoRefGene.ixx
 _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";
   }
   my $whatItDoes = "It cleans up or compresses intermediate files.";
   my $bossScript = newBash HgRemoteScript("$runDir/cleanup.bash", $workhorse,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_
 export db="$db"
 rm -fr $buildDir/target/
 rm -fr $buildDir/blatRun/err/
 rm -fr $buildDir/blatRun/result/
 rm -f $buildDir/blatRun/batch.bak
 rm -f $buildDir/NM.gp
 rm -f $buildDir/NR.gp
 rm -f $buildDir/NM.psl
 rm -f $buildDir/NR.psl
-rm -f $buildDir/\$db.bgpInput
+gzip $buildDir/\$db.bgpInput &
+gzip $buildDir/\$db.ix.txt &
 gzip $buildDir/\$db.all.psl &
 gzip $buildDir/\$db.xenoRefGene.psl &
 gzip $buildDir/\$db.xenoRefGene.gp
 wait
 _EOF_
   );
   $bossScript->execute();
 } # doCleanup
 
 #########################################################################
 # main
 
 # Prevent "Suspended (tty input)" hanging:
 &HgAutomate::closeStdin();