cd52f66464cce415303d7ae24ba28603c927ee4f
hiram
  Thu Mar 6 15:39:33 2025 -0800
better names in ncbiRefSeq track fields and updated related trackDb URLs refs #32704

diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl
index a7ff0a18a67..e2899b22bf1 100755
--- src/hg/utils/automation/doNcbiRefSeq.pl
+++ src/hg/utils/automation/doNcbiRefSeq.pl
@@ -1,1036 +1,1043 @@
 #!/usr/bin/env perl
 
 # DO NOT EDIT the /cluster/bin/scripts copy of this file --
 # edit ~/kent/src/hg/utils/automation/doNcbiRefSeq.pl instead.
 
 use Getopt::Long;
 use warnings;
 use strict;
 use FindBin qw($Bin);
 use lib "$Bin";
 use HgAutomate;
 use HgRemoteScript;
 use HgStepManager;
 
 my $doIdKeys = "$Bin/doIdKeys.pl";
 my $gff3ToRefLink = "$Bin/gff3ToRefLink.pl";
 my $gbffToCds = "$Bin/gbffToCds.pl";
 my $ncbiRefSeqOtherIxIxx = "$Bin/ncbiRefSeqOtherIxIxx.pl";
 my $ncbiRefSeqOtherAttrs = "$Bin/ncbiRefSeqOtherAttrs.pl";
 
 # Option variable names, both common and peculiar to this script:
 use vars @HgAutomate::commonOptionVars;
 use vars @HgStepManager::optionVars;
 use vars qw/
     $opt_buildDir
     $opt_liftFile
     $opt_assemblyHub
     $opt_target2bit
     $opt_toGpWarnOnly
     /;
 
 # Specify the steps supported with -continue / -stop:
 my $stepper = new HgStepManager(
     [ { name => 'download', func => \&doDownload },
       { name => 'process', func => \&doProcess },
       { name => 'load', func => \&doLoad },
       { name => 'cleanup', func => \&doCleanup },
     ]
 				);
 
 # Option defaults:
 my $dbHost = 'hgwdev';
 my $bigClusterHub = 'ku';
 my $smallClusterHub = 'ku';
 my $workhorse = 'hgwdev';
 my $defaultWorkhorse = 'hgwdev';
 my $defaultFileServer = 'hgwdev';
 my $fileServer = 'hgwdev';
 
 my $base = $0;
 $base =~ s/^(.*\/)?//;
 
 sub usage {
   # Usage / help / self-documentation:
   my ($status, $detailed) = @_;
   # Basic help (for incorrect usage):
   print STDERR "
 usage: $base [options] asmId db
 required arguments:
     asmId          - assembly identifier at NCBI FTP site, examples:
                    - GCF_000001405.32_GRCh38.p6 GCF_000001635.24_GRCm38.p4 etc..
     db             - database to load with track tables
 
 options:
 ";
   print STDERR $stepper->getOptionHelp();
   print STDERR <<_EOF_
     -buildDir dir         Use dir instead of default
                           $HgAutomate::clusterData/\$db/$HgAutomate::trackBuild/ncbiRefSeq.\$date
                           (necessary when continuing at a later date).
     -assemblyHub          the processing is taking place in an assembly hub
                           build
     -toGpWarnOnly         add -warnAndContinue to the gff3ToGenePred operation
                           to avoid gene definitions that will not convert
     -liftFile pathName    a lift file to translate NCBI names to local genome
                           names
     -target2bit pathName  when not a local UCSC genome, use this 2bit file for
                           the target genome sequence
 _EOF_
   ;
   print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
 					'workhorse' => $defaultWorkhorse,
 					'fileServer' => $defaultFileServer,
 					'bigClusterHub' => $bigClusterHub,
 					'smallClusterHub' => $smallClusterHub);
   print STDERR "
 Automates UCSC's ncbiRefSeq track build.  Steps:
     download: symlink local files or rsync required files from NCBI FTP site
     process: generate the track data files from the download data
     load: load the processed data into database tables
     cleanup: Removes or compresses intermediate files.
 All operations are performed in the build directory which is
 $HgAutomate::clusterData/\$db/$HgAutomate::trackBuild/ncbiRefSeq.\$date unless -buildDir is given.
 
 Expects to find already done idKeys procedure and result file in:
    /hive/data/genomes/<db>/bed/idKeys/<db>.idKeys.txt
 See also: doIdKeys.pl command.
 ";
   # Detailed help (-help):
   print STDERR "
 Assumptions:
 1. $HgAutomate::clusterData/\$db/\$db.2bit contains RepeatMasked sequence for
    database/assembly \$db.
 2. $HgAutomate::clusterData/\$db/chrom.sizes contains all sequence names and sizes from
    \$db.2bit.
 NOTE: Override these assumptions with the -target2Bit option
 " if ($detailed);
   print "\n";
   exit $status;
 }
 
 
 # Globals:
 # Command line args: asmId db
 my ($asmId, $db);
 # Other:
 my ($ftpDir, $buildDir, $assemblyHub, $toGpWarnOnly, $dbExists, $liftFile, $target2bit);
 my ($secondsStart, $secondsEnd);
 
 sub checkOptions {
   # Make sure command line options are valid/supported.
   my $ok = GetOptions(@HgStepManager::optionSpec,
 		      'buildDir=s',
 		      'liftFile=s',
 		      'target2bit=s',
 		      'assemblyHub',
 		      'toGpWarnOnly',
 		      @HgAutomate::commonOptionSpec,
 		      );
   &usage(1) if (!$ok);
   &usage(0, 1) if ($opt_help);
   &HgAutomate::processCommonOptions();
   my $err = $stepper->processOptions();
   usage(1) if ($err);
   $dbHost = $opt_dbHost if ($opt_dbHost);
   $workhorse = $opt_workhorse if ($opt_workhorse);
   $bigClusterHub = $opt_bigClusterHub if ($opt_bigClusterHub);
   $smallClusterHub = $opt_smallClusterHub if ($opt_smallClusterHub);
   $fileServer = $opt_fileServer if ($opt_fileServer);
 }
 
 #########################################################################
 # * step: download [workhorse]
 sub doDownload {
   my $filesFound = 0;
  my @requiredFiles = qw( genomic.gff.gz rna.fna.gz rna.gbff.gz protein.faa.gz );
   my $filesExpected = scalar(@requiredFiles);
   foreach my $expectFile (@requiredFiles) {
     if ( -s "/hive/data/outside/ncbi/genomes/$ftpDir/${asmId}_${expectFile}" ) {
       ++$filesFound;
     } else {
       printf STDERR "# doNcbiRefSeq.pl: missing required file /hive/data/outside/ncbi/${asmId}_${expectFile}\n";
     }
   }
 
   if ($filesFound < $filesExpected) {
     printf STDERR "# doNcbiRefSeq.pl download: can not find all files required\n";
     exit 255;
   }
   my $runDir = "$buildDir/download";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "download required set of files from NCBI.";
   my $bossScript = newBash HgRemoteScript("$runDir/doDownload.bash", $workhorse,
 				      $runDir, $whatItDoes);
   my $outsideCopy = "/hive/data/outside/ncbi/genomes/$ftpDir";
   # might already have the NCBI 2bit file here:
   my $localData = $buildDir;
   $localData =~ s#trackData/ncbiRefSeq#download#;
   my $local2Bit = "$localData/$asmId.2bit";
 
   # establish variables
   $bossScript->add(<<_EOF_
 # establish all potential variables to use here, not all may be used
 
 export outsideCopy=$outsideCopy
 export asmId=$asmId
 export ftpDir=$ftpDir
 export runDir=$runDir
 export db=$db
 
 _EOF_
     );
 
 printf STDERR "# checking $outsideCopy\n";
 printf STDERR "# checking $local2Bit\n";
 
   # see if local symLinks can be made with copies already here from NCBI:
   if ( -d "$outsideCopy" ) {
     $bossScript->add(<<_EOF_
 # local file copies exist, use symlinks
 
 ln -f -s \$outsideCopy/\${asmId}_genomic.gff.gz .
 ln -f -s \$outsideCopy/\${asmId}_rna.fna.gz .
 ln -f -s \$outsideCopy/\${asmId}_rna.gbff.gz .
 ln -f -s \$outsideCopy/\${asmId}_protein.faa.gz .
 _EOF_
     );
   } else {
     $bossScript->add(<<_EOF_
 # local file copies do not exist, download from NCBI:
 
 for F in _rna.gbff _rna.fna _protein.faa _genomic.gff
 do
    rsync -a -P \\
        rsync://ftp.ncbi.nlm.nih.gov/\$ftpDir/\$asmId\${F}.gz ./
 done
 _EOF_
     );
   }
 
   if ( -s $local2Bit ) {
     $bossScript->add(<<_EOF_
 ln -f -s $local2Bit \${asmId}.ncbi.2bit
 _EOF_
     );
   } elsif ( -s "$outsideCopy/${asmId}_genomic.fna.gz") {
     $bossScript->add(<<_EOF_
 # build \$asmId.ncbi.2bit from local copy of genomic fasta
 
 faToTwoBit \$outsideCopy/\${asmId}_genomic.fna.gz \${asmId}.ncbi.2bit
 _EOF_
     );
   } else {
     $bossScript->add(<<_EOF_
 # download genomic fasta and build \${asmId}.ncbi.2bit
 rsync -a -P \\
        rsync://ftp.ncbi.nlm.nih.gov/\$ftpDir/\${asmId}_genomic.fna.gz ./
 faToTwoBit \${asmId}_genomic.fna.gz \${asmId}.ncbi.2bit
 _EOF_
     );
   }
 
   my $haveLiftFile = 0;
   if ( -s "$liftFile" ) {
        $haveLiftFile = 1;
   } elsif ($dbExists) {
      # check if db.ucscToRefSeq exists?
      my $sql = "show tables like 'ucscToRefSeq';";
      my $result = `hgsql $db -BN -e "$sql"`;
      chomp $result;
      if ( $result =~ m/ucscToRefSeq/ ) {
        $haveLiftFile = 1;
 ### the sort -k2,2 -u eliminates the problem of duplicate sequences existing
 ### in the target $db assembly
        $bossScript->add(<<_EOF_
 cd \$runDir
 hgsql -N -e 'select 0,name,chromEnd,chrom,chromEnd from ucscToRefSeq;' \${db} \\
      | sort -k2,2 -u > \${asmId}To\${db}.lift
 _EOF_
        );
     }
   }
 
   my $dbTwoBit = "$HgAutomate::clusterData/$db/$db.2bit";
   $dbTwoBit = $target2bit if (-s "$target2bit");
 
   if (! $haveLiftFile ) {
      # if this is an assembly hub and it did NOT supply a lift file,
      # then we don't need one, do not attempt to build
      if (! $opt_assemblyHub) {
        $bossScript->add(<<_EOF_
 # generate idKeys for the NCBI sequence to translate names to UCSC equivalents
 
 rm -rf \$runDir/idKeys
 mkdir -p \$runDir/idKeys
 cd \$runDir/idKeys
 time ($doIdKeys -buildDir=\$runDir/idKeys -twoBit=\$runDir/\$asmId.ncbi.2bit \$db) > idKeys.log 2>&1
 cd \$runDir
 twoBitInfo $dbTwoBit stdout | sort -k2,2nr > \$db.chrom.sizes
 ln -f -s idKeys/\$db.idKeys.txt ./ncbi.\$asmId.idKeys.txt
 ln -f -s /hive/data/genomes/\$db/bed/idKeys/\$db.idKeys.txt ./ucsc.\$db.idKeys.txt
 # joining the idKeys establishes a lift file to translate chrom names
 join -t\$'\\t' ucsc.\$db.idKeys.txt ncbi.\$asmId.idKeys.txt \\
    | cut -f2-3 | sort \\
      | join -t\$'\\t' - <(sort \$db.chrom.sizes) \\
        | awk -F\$'\\t' '{printf "0\\t%s\\t%d\\t%s\\t%d\\n", \$2, \$3, \$1, \$3}' \\
           | sort -k3nr > \${asmId}To\${db}.lift
 _EOF_
        );
      }
   }
 
   $bossScript->add(<<_EOF_
 cd \$runDir
 twoBitInfo \$asmId.ncbi.2bit stdout | sort -k2nr > \$asmId.ncbi.chrom.sizes
 zcat \${asmId}_rna.fna.gz | sed -e 's/ .*//;' | gzip -c > \$asmId.rna.fa.gz
 faSize -detailed \${asmId}.rna.fa.gz | sort -k2nr > rna.sizes
 
 # genbank processor extracts infomation about the RNAs
 /hive/data/outside/genbank/bin/x86_64/gbProcess \\
     -inclXMs /dev/null \$asmId.raFile.txt \${asmId}_rna.gbff.gz
 _EOF_
   );
   $bossScript->execute();
 } # doDownload
 
 #########################################################################
 # * step: process [dbHost]
 sub doProcess {
   my $runDir = "$buildDir/process";
   my $downloadDir = "$buildDir/download";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "process NCBI download files into track files.";
   # Use dbHost since genePredCheck -db=$db needs database
   my $bossScript = newBash HgRemoteScript("$runDir/doProcess.bash", $dbHost,
 				      $runDir, $whatItDoes);
 
   my $genePredCheckDb = "genePredCheck -db=\$db";
   if (! $dbExists) {
     $genePredCheckDb = "genePredCheck";
   }
   my $warnOnly = "";
   $warnOnly = "-warnAndContinue" if ($toGpWarnOnly);
 
   my $localLiftFile = "$downloadDir/${asmId}To${db}.lift";
   if (! -s "$localLiftFile") {
      $localLiftFile = "../download/${asmId}To${db}.lift" if (-s "../download/${asmId}To${db}.lift");
   }
   $localLiftFile = "" if (! -s "$localLiftFile");
   $localLiftFile = $liftFile if (-s $liftFile);
   my $pslTargetSizes = "-db=\$db";
   my $fakePslSizes = "";
   if (-s "$target2bit") {
     $pslTargetSizes = "-targetSizes=\$db.chrom.sizes";
     $fakePslSizes = "-chromSize=\$db.chrom.sizes";
   }
 
   my $dbTwoBit = "$HgAutomate::clusterData/$db/$db.2bit";
   $dbTwoBit = $target2bit if (-s "$target2bit");
   my $localSizes = "$HgAutomate::clusterData/$db/chrom.sizes";
 
   $bossScript->add(<<_EOF_
 # establish all variables to use here
 
 export asmId=$asmId
 export downloadDir=$downloadDir
 export ncbiGffGz=\$downloadDir/\${asmId}_genomic.gff.gz
 export db=$db
 export chromSizes="$localSizes"
 export gff3ToRefLink=$gff3ToRefLink
 export gbffToCds=$gbffToCds
 export dateStamp=`date "+%F"`
 if [ -s "../../../\$asmId.chrom.sizes" ]; then
   chromSizes="../../../\$asmId.chrom.sizes"
 fi
 if [ -s "../download/\$asmId.ncbi.chrom.sizes" ]; then
   chromSizes="../download/\$asmId.ncbi.chrom.sizes"
 fi
 
 export annotationRelease=`zcat \$ncbiGffGz | head -100 | grep ^#.annotation-source | sed -e 's/.*annotation-source //; s/ Updated Annotation Release//;'`
 if [ "\$annotationRelease" == "" ]; then
   export annotationRelease=\$asmId
 fi
 export versionDate=`ls -L --full-time \$ncbiGffGz | awk '{print \$6;}'`
 echo "\$annotationRelease (\$versionDate)" > ncbiRefSeqVersion.txt
 
 # this produces the genePred in NCBI coordinates
 # 8/23/17: gff3ToGenePred quits over illegal attribute SO_type... make it legal (so_type):
 if [ -s ../../../download/\${asmId}.remove.dups.list ]; then
   zcat \$ncbiGffGz | grep -v -f ../../../download/\${asmId}.remove.dups.list \\
     | sed -re 's/([;\\t])SO_type=/\\1so_type=/;' \\
       | gff3ToGenePred $warnOnly -refseqHacks -attrsOut=\$asmId.attrs.txt \\
         -unprocessedRootsOut=\$asmId.unprocessedRoots.txt stdin stdout \\
       | genePredFilter -chromSizes=\$chromSizes stdin \$asmId.gp
 else
   zcat \$ncbiGffGz \\
     | sed -re 's/([;\\t])SO_type=/\\1so_type=/;' \\
       | gff3ToGenePred $warnOnly -refseqHacks -attrsOut=\$asmId.attrs.txt \\
         -unprocessedRootsOut=\$asmId.unprocessedRoots.txt stdin stdout \\
       | genePredFilter -chromSizes=\$chromSizes stdin \$asmId.gp
 fi
 genePredCheck \$asmId.gp
 
 rm -f \$asmId.refseqSelectTranscripts.txt
 zegrep 'tag=(RefSeq|MANE) Select' \$ncbiGffGz > before.cut9.txt || true
 
 if [ -s before.cut9.txt ]; then
   cut -f9- before.cut9.txt | tr ';' '\\n' \\
     | grep 'Name=' | grep -v NP_ | cut -d= -f2 | sort -u \\
        > \$asmId.refseqSelectTranscripts.txt
 fi
 rm -f before.cut9.txt
 
 # extract labels from semi-structured text in gbff COMMENT/description sections:
 zcat \$downloadDir/\${asmId}_rna.gbff.gz \\
   | (grep ' :: ' || true) \\
     | perl -wpe 's/\\s+::.*//; s/^\\s+//;' \\
       | sort -u \\
         > pragmaLabels.txt
 
 # extract cross reference text for refLink
 \$gff3ToRefLink \$downloadDir/\$asmId.raFile.txt \$ncbiGffGz pragmaLabels.txt 2> \$db.refLink.stderr.txt \\
   | sort > \$asmId.refLink.tab
 
 _EOF_
   );
   if ( -s "$localLiftFile") {
   $bossScript->add(<<_EOF_
 # converting the NCBI coordinates to UCSC coordinates
 liftUp -extGenePred -type=.gp stdout $localLiftFile warn \$asmId.gp \\
   | gzip -c > \$asmId.\$db.gp.gz
 _EOF_
   );
   } else {
   $bossScript->add(<<_EOF_
 # no lifting necessary
 cat \$asmId.gp | gzip -c > \$asmId.\$db.gp.gz
 _EOF_
   );
   }
   $bossScript->add(<<_EOF_
 $genePredCheckDb \$asmId.\$db.gp.gz
 zcat \$asmId.\$db.gp.gz > ncbiRefSeq.\$dateStamp
 genePredToGtf -utr file ncbiRefSeq.\$dateStamp stdout | gzip -c \\
   > ../\$db.\$dateStamp.ncbiRefSeq.gtf.gz
 rm -f ncbiRefSeq.\$dateStamp
 
 # curated subset of all genes
 (zegrep "^[NY][MRP]_" \$asmId.\$db.gp.gz || true) > \$db.curated.gp
 # may not be any curated genes
 if [ ! -s \$db.curated.gp ]; then
   rm -f \$db.curated.gp
   rm -f \$db.refseqSelect.curated.gp
   rm -f hgmd.curated.gp
 else
   if [ -s \$asmId.refseqSelectTranscripts.txt ]; then
     cat \$db.curated.gp | fgrep -f \$asmId.refseqSelectTranscripts.txt - \\
       > \$db.refseqSelect.curated.gp
     # may not be any refseqSelect.curated genes
     if [ ! -s \$db.refseqSelect.curated.gp ]; then
       rm -f \$db.refseqSelect.curated.gp
     fi
   fi
   if [ \$db = "hg19" -o \$db = "hg38" ]; then
      hgmdFile=`ls /hive/data/outside/hgmd/20*.4-hgmd-public_hg38.tsv | tail -1`
      if [ -s "\$hgmdFile" ]; then
        cut -f7 "\$hgmdFile" | cut -d. -f1 | sort -u | awk '{printf "%s.\\n", \$1}' > hgmdTranscripts.txt
        fgrep -f hgmdTranscripts.txt \$db.curated.gp > hgmd.curated.gp
      fi
   fi
 fi
 
 # predicted subset of all genes
 (zegrep "^X[MR]_" \$asmId.\$db.gp.gz || true) > \$db.predicted.gp
 
 # not curated or predicted subset of all genes, the left overs
 (zegrep -v "^[NXY][MRP]_" \$asmId.\$db.gp.gz || true) > \$db.other.gp
 
 # curated and predicted without leftovers:
 (zegrep "^[NXY][MRP]_" \$asmId.\$db.gp.gz || true) > \$db.ncbiRefSeq.gp
 
 if [ -s \$db.curated.gp ]; then
   $genePredCheckDb \$db.curated.gp
   if [ -s \$db.refseqSelect.curated.gp ]; then
      $genePredCheckDb \$db.refseqSelect.curated.gp
   fi
   if [ -s hgmd.curated.gp ]; then
      $genePredCheckDb hgmd.curated.gp
   fi
 fi
 if [ -s \$db.predicted.gp ]; then
   $genePredCheckDb \$db.predicted.gp
 fi
 if [ -s \$db.other.gp ]; then
   $genePredCheckDb \$db.other.gp
 fi
 
 # join the refLink metadata with curated+predicted names
 cut -f1 \$db.ncbiRefSeq.gp | sort -u > \$asmId.\$db.name.list
 join -t\$'\\t' \$asmId.\$db.name.list \$asmId.refLink.tab > \$asmId.\$db.ncbiRefSeqLink.tab
 
 # Make bigBed with attributes in extra columns for ncbiRefSeqOther:
 twoBitInfo $dbTwoBit stdout | sort -k2,2n > \$db.chrom.sizes
 
 if [ -s \$db.other.gp ]; then
   if [ -s ../../../download/\${asmId}.remove.dups.list ]; then
     genePredToBed -tab -fillSpace \$db.other.gp stdout | sort -k1,1 -k2n,2n \\
       | grep -v -f ../../../download/\${asmId}.remove.dups.list > \$db.other.bed
   else
     genePredToBed -tab -fillSpace \$db.other.gp stdout | sort -k1,1 -k2n,2n > \$db.other.bed
   fi
   $ncbiRefSeqOtherAttrs \$db.other.bed \$asmId.attrs.txt > \$db.other.extras.bed
   bedToBigBed -type=bed12+13 -as=ncbiRefSeqOther.as -tab \\
     -extraIndex=name \\
     \$db.other.extras.bed \$db.chrom.sizes \$db.other.bb
 
   # Make trix index for ncbiRefSeqOther
   $ncbiRefSeqOtherIxIxx \\
     ncbiRefSeqOther.as \$db.other.extras.bed > ncbiRefSeqOther.ix.tab
 
   ixIxx ncbiRefSeqOther.ix.tab ncbiRefSeqOther.ix{,x}
 fi
 
 # PSL data will be loaded into a psl type track to show the alignments
 (zgrep "^#" \$ncbiGffGz | head || true) > gffForPsl.gff
 if [ -s ../../../download/\${asmId}.remove.dups.list ]; then
   (zegrep -v "NG_" \$ncbiGffGz || true) \\
     | grep -v -f ../../../download/\${asmId}.remove.dups.list \\
     | awk -F\$'\\t' '\$3 == "cDNA_match" || \$3 == "match"' >> gffForPsl.gff
   gff3ToPsl -dropT \$downloadDir/\$asmId.ncbi.chrom.sizes \$downloadDir/rna.sizes \\
     gffForPsl.gff stdout | pslPosTarget stdin \$asmId.psl
 else
   (zegrep -v "NG_" \$ncbiGffGz || true) \\
     | awk -F\$'\\t' '\$3 == "cDNA_match" || \$3 == "match"' >> gffForPsl.gff
   gff3ToPsl -dropT \$downloadDir/\$asmId.ncbi.chrom.sizes \$downloadDir/rna.sizes \\
     gffForPsl.gff stdout | pslPosTarget stdin \$asmId.psl
 fi
 # might be empty result
 if [ ! -s \$asmId.psl ]; then
   rm -f \$asmId.psl
 else
 _EOF_
   );
   # note else clause of above if statement is concluded below in these two
   # cases
   if ( -s "$localLiftFile") {
   $bossScript->add(<<_EOF_
  simpleChain -outPsl -maxGap=300000 \$asmId.psl stdout | pslSwap stdin stdout \\
    | liftUp -type=.psl stdout $localLiftFile warn stdin \\
      | gzip -c > \$db.psl.gz
 fi
 _EOF_
   );
   } else {
   $bossScript->add(<<_EOF_
  simpleChain -outPsl -maxGap=300000 \$asmId.psl stdout | pslSwap stdin stdout \\
     | gzip -c > \$db.psl.gz
 fi
 _EOF_
   );
   }
 
   $bossScript->add(<<_EOF_
 if [ -s \$db.psl.gz ]; then
   pslCheck $pslTargetSizes \\
     -querySizes=\$downloadDir/rna.sizes \$db.psl.gz
 fi
 
 # extract RNA CDS information from genbank record
 # Note: $asmId.raFile.txt could be used instead of _rna.gbff.gz
 \$gbffToCds \$downloadDir/\${asmId}_rna.gbff.gz | sort > \$asmId.rna.cds
 
 # the NCBI _genomic.gff.gz file only contains cDNA_match records for transcripts
 # that do not *exactly* match the reference genome.  For all other transcripts
 # construct 'fake' PSL records representing the alignments of all cDNAs
 # that would be perfect matches to the reference genome.  The pslFixCdsJoinGap
 # will fixup those records with unusual alignments due to frameshifts of
 # various sorts as found in the rna.cds file:
 genePredToFakePsl -qSizes=\$downloadDir/rna.sizes $fakePslSizes \$db \$db.ncbiRefSeq.gp \\
   stdout \$db.fake.cds \\
      | pslFixCdsJoinGap stdin \$asmId.rna.cds \$db.fake.psl
 if [ -s \$db.psl.gz ]; then
   pslCat -nohead \$db.psl.gz | cut -f10,14 > \$db.psl.names
 fi
 if [ -s \$db.psl.names ]; then
   pslSomeRecords -tToo -not \$db.fake.psl \$db.psl.names \$db.someRecords.psl
 else
   cp -p \$db.fake.psl \$db.someRecords.psl
 fi
 if [ -s \$db.psl.gz ]; then
   pslSort dirs stdout \\
    ./tmpdir \$db.psl.gz \$db.someRecords.psl | gzip -c > \$db.sorted.psl.gz
 else
   pslSort dirs stdout \\
    ./tmpdir \$db.someRecords.psl | gzip -c > \$db.sorted.psl.gz
 fi
 (pslCheck -quiet $pslTargetSizes -pass=stdout -fail=\$asmId.\$db.fail.psl \$db.sorted.psl.gz || true) \\
     | pslPosTarget stdin stdout \\
     | pslRecalcMatch -ignoreQMissing stdin $dbTwoBit \$downloadDir/\$asmId.rna.fa.gz stdout \\
      | sort -k14,14 -k16,16n | gzip -c > \$asmId.\$db.psl.gz
 rm -fr ./tmpdir
 pslCheck $pslTargetSizes \$asmId.\$db.psl.gz
 _EOF_
   );
   $bossScript->execute();
 } # doProcess
 
 #########################################################################
 # * step: load [dbHost]
 sub doLoad {
   my $runDir = "$buildDir";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "load NCBI processed files into track files.";
   my $bossScript = newBash HgRemoteScript("$runDir/doLoad.bash", $dbHost,
 				      $runDir, $whatItDoes);
 
   my $gbdbDir = "$HgAutomate::gbdb/\$db/ncbiRefSeq";
   my $dbTwoBit = "$HgAutomate::clusterData/$db/$db.2bit";
   $dbTwoBit = $target2bit if (-s "$target2bit");
 
   my $genePredCheckDb = "genePredCheck -db=\$db";
   if (! $dbExists) {
     $genePredCheckDb = "genePredCheck";
   }
 
   my $verString = `cat $buildDir/process/ncbiRefSeqVersion.txt`;
   chomp $verString;
   $verString =~ s/.*elease //;
   $verString =~ s/^[^0-9]*//;
   $verString =~ s/ .*//;
 
   $bossScript->add(<<_EOF_
 # establish all variables to use here
 
 export db="$db"
 export asmId="$asmId"
 export verString="$verString"
 
 _EOF_
   );
   if (! $dbExists) {
     $bossScript->add(<<_EOF_
 export target2bit=$dbTwoBit
 
 twoBitInfo \$target2bit stdout | sort -k2,2nr > \$db.chrom.sizes
 wget -O bigGenePred.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigGenePred.as'
 wget -O bigPsl.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/bigPsl.as'
 
 ### overall gene track with both predicted and curated
-genePredToBigGenePred process/\$db.ncbiRefSeq.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeq.bigGp
+\$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+       process/\$db.ncbiRefSeq.gp | sort -k1,1 -k2,2n > \$db.ncbiRefSeq.bigGp
 genePredToBed -tab -fillSpace process/\$db.ncbiRefSeq.gp stdout \\
     | bedToExons stdin stdout | bedSingleCover.pl stdin > \$asmId.exons.bed
 export baseCount=`awk '{sum+=\$3-\$2}END{printf "%d", sum}' \$asmId.exons.bed`
 export asmSizeNoGaps=`grep sequences ../../\$asmId.faSize.txt | awk '{print \$5}'`
 export perCent=`echo \$baseCount \$asmSizeNoGaps | awk '{printf "%.3f", 100.0*\$1/\$2}'`
 bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
   \$db.ncbiRefSeq.bigGp \$db.chrom.sizes \\
     \$db.ncbiRefSeq.bb
 bigBedInfo \$db.ncbiRefSeq.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$db.ncbiRefSeq.stats.txt
 LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeq %s %'d %s %'d\\n" `cat \$db.ncbiRefSeq.stats.txt` | xargs echo
 ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.ncbiRefSeq.gp \\
     | sort -u > \$db.ncbiRefSeq.ix.txt
 ixIxx \$db.ncbiRefSeq.ix.txt \$db.ncbiRefSeq.ix{,x}
 rm -f \$db.ncbiRefSeq.ix.txt
 
 ### curated only if present
 if [ -s process/\$db.curated.gp ]; then
-  genePredToBigGenePred process/\$db.curated.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeqCurated.bigGp
+  \$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+     process/\$db.curated.gp | sort -k1,1 -k2,2n > \$db.ncbiRefSeqCurated.bigGp
   bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
   \$db.ncbiRefSeqCurated.bigGp \$db.chrom.sizes \\
     \$db.ncbiRefSeqCurated.bb
   rm -f \$db.ncbiRefSeqCurated.bigGp
   bigBedInfo \$db.ncbiRefSeqCurated.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$db.ncbiRefSeqCurated.stats.txt
   LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqCurated %s %'d %s %'d\\n" `cat \$db.ncbiRefSeqCurated.stats.txt` | xargs echo
   ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.curated.gp \\
     | sort -u > \$db.ncbiRefSeqCurated.ix.txt
   ixIxx \$db.ncbiRefSeqCurated.ix.txt \$db.ncbiRefSeqCurated.ix{,x}
   rm -f \$db.ncbiRefSeqCurated.ix.txt
 ### and refseqSelect if exists (a subset of curated)
   if [ -s process/\$db.refseqSelect.curated.gp ]; then
-    genePredToBigGenePred process/\$db.refseqSelect.curated.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeqSelectCurated.bigGp
+    \$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+      process/\$db.refseqSelect.curated.gp | sort -k1,1 -k2,2n \\
+         > \$db.ncbiRefSeqSelectCurated.bigGp
     bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
     \$db.ncbiRefSeqSelectCurated.bigGp \$db.chrom.sizes \\
       \$db.ncbiRefSeqSelectCurated.bb
     rm -f \$db.ncbiRefSeqSelectCurated.bigGp
     bigBedInfo \$db.ncbiRefSeqSelectCurated.bb | egrep "^itemCount:|^basesCovered:" \\
       | sed -e 's/,//g' > \$db.ncbiRefSeqSelectCurated.stats.txt
     LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqSelectCurated %s %'d %s %'d\\n" `cat \$db.ncbiRefSeqSelectCurated.stats.txt` | xargs echo
     ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.refseqSelect.curated.gp \\
       | sort -u > \$db.ncbiRefSeqSelectCurated.ix.txt
     ixIxx \$db.ncbiRefSeqSelectCurated.ix.txt \$db.ncbiRefSeqSelectCurated.ix{,x}
     rm -f \$db.ncbiRefSeqSelectCurated.ix.txt
   fi
 ### and hgmd if exists (a subset of curated)
   if [ -s process/hgmd.curated.gp ]; then
-    genePredToBigGenePred process/hgmd.curated.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeqHgmd.bigGp
+    \$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+      process/hgmd.curated.gp | sort -k1,1 -k2,2n > \$db.ncbiRefSeqHgmd.bigGp
     bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
     \$db.ncbiRefSeqHgmd.bigGp \$db.chrom.sizes \\
       \$db.ncbiRefSeqHgmd.bb
     rm -f \$db.ncbiRefSeqHgmd.bigGp
     bigBedInfo \$db.ncbiRefSeqHgmd.bb | egrep "^itemCount:|^basesCovered:" \\
       | sed -e 's/,//g' > \$db.ncbiRefSeqHgmd.stats.txt
     LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqHgmd %s %'d %s %'d\\n" `cat \$db.ncbiRefSeqHgmd.stats.txt` | xargs echo
     ~/kent/src/hg/utils/automation/gpToIx.pl process/hgmd.curated.gp \\
       | sort -u > \$db.ncbiRefSeqHgmd.ix.txt
     ixIxx \$db.ncbiRefSeqHgmd.ix.txt \$db.ncbiRefSeqHgmd.ix{,x}
     rm -f \$db.ncbiRefSeqHgmd.ix.txt
   fi
 fi
 
 ### predicted only if present
 if [ -s process/\$db.predicted.gp ]; then
-  genePredToBigGenePred process/\$db.predicted.gp stdout | sort -k1,1 -k2,2n > \$db.ncbiRefSeqPredicted.bigGp
+  \$HOME/kent/src/hg/utils/automation/updateName2.pl process/\$db.attrs.txt \\
+      process/\$db.predicted.gp | sort -k1,1 -k2,2n \\
+        > \$db.ncbiRefSeqPredicted.bigGp
   bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as -extraIndex=name \\
   \$db.ncbiRefSeqPredicted.bigGp \$db.chrom.sizes \\
     \$db.ncbiRefSeqPredicted.bb
   rm -f \$db.ncbiRefSeqPredicted.bigGp
   bigBedInfo \$db.ncbiRefSeqPredicted.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$db.ncbiRefSeqPredicted.stats.txt
   LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqPredicted %s %'d %s %'d\\n" `cat \$db.ncbiRefSeqPredicted.stats.txt` | xargs echo
   ~/kent/src/hg/utils/automation/gpToIx.pl process/\$db.predicted.gp \\
     | sort -u > \$db.ncbiRefSeqPredicted.ix.txt
   ixIxx \$db.ncbiRefSeqPredicted.ix.txt \$db.ncbiRefSeqPredicted.ix{,x}
   rm -f \$db.ncbiRefSeqPredicted.ix.txt
 fi
 
 ### all other annotations, not necessarily genes
 if [ -s "process/\$db.other.bb" ]; then
   ln -f -s process/\$db.other.bb \$db.ncbiRefSeqOther.bb
   bigBedInfo \$db.ncbiRefSeqOther.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$db.ncbiRefSeqOther.stats.txt
   LC_NUMERIC=en_US /usr/bin/printf "# ncbiRefSeqOther %s %'d %s %'d\\n" `cat \$asmId.ncbiRefSeqOther.stats.txt` | xargs echo
 fi
 if [ -s "process/ncbiRefSeqOther.ix" ]; then
   ln -f -s process/ncbiRefSeqOther.ix ./\$db.ncbiRefSeqOther.ix
   ln -f -s process/ncbiRefSeqOther.ixx ./\$db.ncbiRefSeqOther.ixx
 fi
 ln -f -s process/ncbiRefSeqVersion.txt ./\$db.ncbiRefSeqVersion.txt
 # select only coding genes to have CDS records
 
 awk -F" " '\$6 != \$7 {print \$1;}' process/\$db.ncbiRefSeq.gp \\
   | sort -u > coding.cds.name.list
 
 join -t\$'\t' coding.cds.name.list process/\$asmId.rna.cds \\
   > \$db.ncbiRefSeqCds.tab
 
 rm -f coding.cds.name.list
 
 ln -f -s process/\$asmId.\$db.ncbiRefSeqLink.tab .
 cut -f6 \$asmId.\$db.ncbiRefSeqLink.tab | grep . \\
   | sort -u > \$db.ncbiRefSeqLink.protAcc.list
 
 zcat download/\${asmId}_protein.faa.gz \\
    | sed -e 's/ .*//;' | faToTab -type=protein -keepAccSuffix stdin stdout \\
      | sort | join -t\$'\\t' \$db.ncbiRefSeqLink.protAcc.list - \\
         > \$db.ncbiRefSeqPepTable.tab
 
 # and load the fasta peptides, again, only those for items that exist
 pslCat -nohead process/\$asmId.\$db.psl.gz | cut -f10 \\
    | sort -u > \$db.psl.used.rna.list
 cut -f5 process/\$asmId.\$db.ncbiRefSeqLink.tab \\
    | grep . | sort -u > \$db.mrnaAcc.name.list
 sort -u \$db.psl.used.rna.list \$db.mrnaAcc.name.list > \$db.rna.select.list
 cut -f1 process/\$db.ncbiRefSeq.gp | sort -u > \$db.gp.name.list
 comm -12 \$db.rna.select.list \$db.gp.name.list > \$db.toLoad.rna.list
 comm -23 \$db.rna.select.list \$db.gp.name.list > \$db.not.used.rna.list
 faSomeRecords download/\$asmId.rna.fa.gz \$db.toLoad.rna.list \$db.rna.fa
 grep '^>' \$db.rna.fa | sed -e 's/^>//' | sort > \$db.rna.found.list
 comm -13 \$db.rna.found.list \$db.gp.name.list > \$db.noRna.available.list
 
 _EOF_
     );
 
   my $nonNucNames="chrM";
 
   my $haveLiftFile = 0;
   if ( -s "$liftFile" ) {
        $haveLiftFile = 1;
   }
   # if this is an assembly hub, find out what the non-nuclear names are
   if ( $opt_assemblyHub) {
      if ( -s "../../sequence/$asmId.nonNucChr.names") {
      # with lift file means to use UCSC name in the nonNucChr.names
      if ($haveLiftFile ) {
         $nonNucNames=`cut -f1 ../../sequence/$asmId.nonNucChr.names | xargs echo | tr ' ' '|'`;
      } else {
         $nonNucNames=`cut -f2 ../../sequence/$asmId.nonNucChr.names | xargs echo | tr ' ' '|'`;
      }
      chomp $nonNucNames;
      }
   }
      # if this is an assembly hub and it did NOT supply a lift file,
      # then we don't need one, do not attempt to build
     $bossScript->add(<<_EOF_
 
 # If \$db.noRna.available.list is not empty but items are on chrM,
 # make fake cDNA sequence for them using chrM sequence
 # since NCBI puts proteins, not coding RNAs, in the GFF.
 if [ -s \$db.noRna.available.list ]; then
   pslCat -nohead process/\$asmId.\$db.psl.gz \\
     | grep -Fwf \$db.noRna.available.list \\
       | egrep "$nonNucNames" > missingChrMFa.psl
   if [ -s missingChrMFa.psl ]; then
     pslToBed missingChrMFa.psl stdout \\
       | twoBitToFa -bed=stdin \$target2bit stdout >> \$db.rna.fa
   fi
 fi
 
 if [ -s process/\$asmId.rna.cds ]; then
   cat process/\$asmId.rna.cds | grep '[0-9]\\+\\.\\.[0-9]\\+' \\
     | pslMismatchGapToBed -cdsFile=stdin -db=\$db -ignoreQNamePrefix=X \\
       process/\$asmId.\$db.psl.gz \$target2bit \\
         \$db.rna.fa ncbiRefSeqGenomicDiff || true
 
   if [ -s ncbiRefSeqGenomicDiff.bed ]; then
     wget -O txAliDiff.as 'https://raw.githubusercontent.com/ucscGenomeBrowser/kent/refs/heads/master/src/hg/lib/txAliDiff.as'
     bedToBigBed -type=bed9+ -tab -as=txAliDiff.as \\
       ncbiRefSeqGenomicDiff.bed \$db.chrom.sizes ncbiRefSeqGenomicDiff.bb
   else
     rm -f ncbiRefSeqGenomicDiff.bed
   fi
 fi
 
 export totalBases=`ave -col=2 \$db.chrom.sizes | grep "^total" | awk '{printf "%d", \$2}'`
 export basesCovered=`bedSingleCover.pl \$db.ncbiRefSeq.bigGp | ave -col=4 stdin | grep "^total" | awk '{printf "%d", \$2}'`
 export percentCovered=`echo \$basesCovered \$totalBases | awk '{printf "%.3f", 100.0*\$1/\$2}'`
 printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" \\
    "\$totalBases" "\$percentCovered" > fb.ncbiRefSeq.\$db.txt
 printf "%d bases of %d (%s%%) in intersection\\n" "\$baseCount" "\$asmSizeNoGaps" "\$perCent" > fb.\$asmId.ncbiRefSeq.txt
 
 rm -f \$db.ncbiRefSeq.bigGp \$asmId.exons.bed
 
 pslToBigPsl -fa=download/\$asmId.rna.fa.gz -cds=process/\$asmId.rna.cds \\
   process/\$asmId.\$db.psl.gz stdout | sort -k1,1 -k2,2n > \$db.bigPsl
 bedToBigBed -type=bed12+13 -tab -as=bigPsl.as -extraIndex=name \\
   \$db.bigPsl \$db.chrom.sizes \$db.bigPsl.bb
 rm -f \$db.bigPsl
 _EOF_
     );
   } else {	# processing for a database genome
 
     $bossScript->add(<<_EOF_
 # loading the genePred tracks, all genes in one, and subsets
 hgLoadGenePred -genePredExt \$db ncbiRefSeq process/\$db.ncbiRefSeq.gp
 $genePredCheckDb ncbiRefSeq
 
 if [ -s process/\$db.curated.gp ]; then
   hgLoadGenePred -genePredExt \$db ncbiRefSeqCurated process/\$db.curated.gp
   $genePredCheckDb ncbiRefSeqCurated
   if [ -s process/\$db.refseqSelect.curated.gp ]; then
     hgLoadGenePred -genePredExt \$db ncbiRefSeqSelect process/\$db.refseqSelect.curated.gp
     $genePredCheckDb ncbiRefSeqSelect
   fi
   if [ -s process/hgmd.curated.gp ]; then
     hgLoadGenePred -genePredExt \$db ncbiRefSeqHgmd process/hgmd.curated.gp
     $genePredCheckDb ncbiRefSeqHgmd
   fi
 fi
 
 if [ -s process/\$db.predicted.gp ]; then
   hgLoadGenePred -genePredExt \$db ncbiRefSeqPredicted process/\$db.predicted.gp
   $genePredCheckDb ncbiRefSeqPredicted
 fi
 
 mkdir -p $gbdbDir
 ln -f -s `pwd`/process/\$db.other.bb $gbdbDir/ncbiRefSeqOther.bb
 hgBbiDbLink \$db ncbiRefSeqOther $gbdbDir/ncbiRefSeqOther.bb
 ln -f -s `pwd`/process/ncbiRefSeqOther.ix{,x} $gbdbDir/
 ln -f -s `pwd`/process/ncbiRefSeqVersion.txt $gbdbDir/
 
 # select only coding genes to have CDS records
 
 awk -F\$'\\t' '\$6 != \$7 {print \$1;}' process/\$db.ncbiRefSeq.gp \\
   | sort -u > coding.cds.name.list
 
 join -t\$'\\t' coding.cds.name.list process/\$asmId.rna.cds \\
   | hgLoadSqlTab \$db ncbiRefSeqCds ~/kent/src/hg/lib/cdsSpec.sql stdin
 
 # loading the cross reference data
 hgLoadSqlTab \$db ncbiRefSeqLink ~/kent/src/hg/lib/ncbiRefSeqLink.sql \\
   process/\$asmId.\$db.ncbiRefSeqLink.tab
 
 # prepare Pep table, select only those peptides that match loaded items
 hgsql -N -e 'select protAcc from ncbiRefSeqLink;' \$db | grep . \\
    | sort -u > \$db.ncbiRefSeqLink.protAcc.list
 
 zcat download/\${asmId}_protein.faa.gz \\
    | sed -e 's/ .*//;' | faToTab -type=protein -keepAccSuffix stdin stdout \\
      | sort | join -t\$'\\t' \$db.ncbiRefSeqLink.protAcc.list - \\
         > \$db.ncbiRefSeqPepTable.tab
 
 hgLoadSqlTab \$db ncbiRefSeqPepTable ~/kent/src/hg/lib/pepPred.sql \\
    \$db.ncbiRefSeqPepTable.tab
 
 # and load the fasta peptides, again, only those for items that exist
 pslCat -nohead process/\$asmId.\$db.psl.gz | cut -f10 \\
    | sort -u > \$db.psl.used.rna.list
 cut -f5 process/\$asmId.\$db.ncbiRefSeqLink.tab | grep . | sort -u > \$db.mrnaAcc.name.list
 sort -u \$db.psl.used.rna.list \$db.mrnaAcc.name.list > \$db.rna.select.list
 cut -f1 process/\$db.ncbiRefSeq.gp | sort -u > \$db.gp.name.list
 comm -12 \$db.rna.select.list \$db.gp.name.list > \$db.toLoad.rna.list
 comm -23 \$db.rna.select.list \$db.gp.name.list > \$db.not.used.rna.list
 faSomeRecords download/\$asmId.rna.fa.gz \$db.toLoad.rna.list \$db.rna.fa
 grep '^>' \$db.rna.fa | sed -e 's/^>//' | sort > \$db.rna.found.list
 comm -13 \$db.rna.found.list \$db.gp.name.list > \$db.noRna.available.list
 
 # If $db.noRna.available.list is not empty but items are on chrM, make fake cDNA sequence
 # for them using chrM sequence since NCBI puts proteins, not coding RNAs, in the GFF.
 if [ -s \$db.noRna.available.list ]; then
   pslCat -nohead process/\$asmId.\$db.psl.gz \\
     | grep -Fwf \$db.noRna.available.list \\
       | grep chrM > missingChrMFa.psl
   if [ -s missingChrMFa.psl ]; then
     pslToBed missingChrMFa.psl stdout \\
       | twoBitToFa -bed=stdin $dbTwoBit stdout >> \$db.rna.fa
   fi
 fi
 
 mkdir -p $gbdbDir
 ln -f -s `pwd`/\$db.rna.fa $gbdbDir/seqNcbiRefSeq.rna.fa
 hgLoadSeq -drop -seqTbl=seqNcbiRefSeq -extFileTbl=extNcbiRefSeq \$db $gbdbDir/seqNcbiRefSeq.rna.fa
 
 hgLoadPsl \$db -table=ncbiRefSeqPsl process/\$asmId.\$db.psl.gz
 
 if [ -s process/\$asmId.rna.cds ]; then
   cat process/\$asmId.rna.cds | grep '[0-9]\\+\\.\\.[0-9]\\+' \\
     | pslMismatchGapToBed -cdsFile=stdin -db=\$db -ignoreQNamePrefix=X \\
       process/\$asmId.\$db.psl.gz $dbTwoBit \\
         \$db.rna.fa ncbiRefSeqGenomicDiff || true
 
   rm -f $gbdbDir/ncbiRefSeqGenomicDiff.bb
   if [ -s ncbiRefSeqGenomicDiff.bed ]; then
     bedToBigBed -type=bed9+ -tab -as=\${HOME}/kent/src/hg/lib/txAliDiff.as \\
       ncbiRefSeqGenomicDiff.bed process/\$db.chrom.sizes ncbiRefSeqGenomicDiff.bb
     ln -s `pwd`/ncbiRefSeqGenomicDiff.bb $gbdbDir/ncbiRefSeqGenomicDiff.bb
   else
     rm -f ncbiRefSeqGenomicDiff.bed
   fi
 fi
 
 if [ -d "/usr/local/apache/htdocs-hgdownload/goldenPath/archive" ]; then
  mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/archive/\$db/ncbiRefSeq/\$verString
  rm -f /usr/local/apache/htdocs-hgdownload/goldenPath/archive/\$db/ncbiRefSeq/\$verString/\$db.\$verString.ncbiRefSeq.gtf.gz
  ln -s `pwd`/\$db.*.ncbiRefSeq.gtf.gz \\
    /usr/local/apache/htdocs-hgdownload/goldenPath/archive/\$db/ncbiRefSeq/\$verString/\$db.\$verString.ncbiRefSeq.gtf.gz
 fi
 
 export DS=`date "+%%F"`
 export gpDir="/usr/local/apache/htdocs-hgdownload/goldenPath/\$db/bigZips/genes"
 rm -f \$gpDir/\$db.ncbiRefSeq.gtf.gz
 mkdir -p \$gpDir
 ln -s `pwd`/\$db.*.ncbiRefSeq.gtf.gz \$gpDir/\$db.ncbiRefSeq.gtf.gz
 export md5Sum="\$gpDir/md5sum.txt"
 export here=`pwd`
 if [ -s "\$md5Sum" ]; then
   origSum=`realpath \$md5Sum`
   bakFile="\${origSum}.\$DS"
   if [! -s "\$bakFile" ]; then
     mv \$origSum \$bakFile
     cd \$gpDir
     md5sum *gz > \$origSum
   fi
 fi
 cd \$here
 featureBits \$db ncbiRefSeq > fb.ncbiRefSeq.\$db.txt 2>&1
 cat fb.ncbiRefSeq.\$db.txt 2>&1
 _EOF_
     );
   }	#	if ($dbExists)
   $bossScript->execute();
 } # doLoad
 
 #########################################################################
 # * step: cleanup [fileServer]
 sub doCleanup {
   my $runDir = "$buildDir";
   my $whatItDoes = "It cleans up or compresses intermediate files.";
   my $bossScript = new HgRemoteScript("$runDir/doCleanup.csh", $fileServer,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_
 gzip -f download/{rna.sizes,*.raFile.txt}
 gzip -f process/*.{tab,txt,gp,gff,psl,cds,bed}
 rm -f $asmId.$db.ncbiRefSeqLink.tab
 ln -f -s process/$asmId.$db.ncbiRefSeqLink.tab.gz .
 # Leave this one uncompressed, gbdb links to it:
 gunzip process/ncbiRefSeqVersion.txt.gz
 _EOF_
   );
   $bossScript->execute();
 } # doCleanup
 
 
 #########################################################################
 # main
 
 # Prevent "Suspended (tty input)" hanging:
 &HgAutomate::closeStdin();
 
 # Make sure we have valid options and exactly 1 argument:
 &checkOptions();
 &usage(1) if (scalar(@ARGV) != 2);
 
 $toGpWarnOnly = 0;
 $toGpWarnOnly = 1 if ($opt_toGpWarnOnly);
 $liftFile = $opt_liftFile ? $opt_liftFile : "";
 $target2bit = $opt_target2bit ? $opt_target2bit : "";
 
 $secondsStart = `date "+%s"`;
 chomp $secondsStart;
 
 # expected command line arguments after options are processed
 ($asmId, $db) = @ARGV;
 # yes, there can be more than two fields separated by _
 # but in this case, we only care about the first two:
 # GC[AF]_123456789.3_assembly_Name
 #   0         1         2      3 ....
 my @partNames = split('_', $asmId);
 $ftpDir = sprintf("%s/%s/%s/%s/%s", $partNames[0],
    substr($partNames[1],0,3), substr($partNames[1],3,3),
    substr($partNames[1],6,3), $asmId);
 
 if ( -z "$liftFile" && ! -s "/hive/data/genomes/$db/bed/idKeys/$db.idKeys.txt") {
   die "ERROR: can not find /hive/data/genomes/$db/bed/idKeys/$db.idKeys.txt\n\t  need to run doIdKeys.pl for $db before this procedure.";
 }
 
 # Force debug and verbose until this is looking pretty solid:
 # $opt_debug = 1;
 # $opt_verbose = 3 if ($opt_verbose < 3);
 
 # Establish what directory we will work in.
 my $date = `date +%Y-%m-%d`;
 chomp $date;
 $buildDir = $opt_buildDir ? $opt_buildDir :
   "$HgAutomate::clusterData/$db/$HgAutomate::trackBuild/ncbiRefSeq.$date";
 
 # may be working on a 2bit file that does not have a database browser
 $dbExists = 0;
 if (! $opt_assemblyHub) {
   $dbExists = 1 if (&HgAutomate::databaseExists($dbHost, $db));
 }
 
 # Do everything.
 $stepper->execute();
 
 $secondsEnd = `date "+%s"`;
 chomp $secondsEnd;
 my $elapsedSeconds = $secondsEnd - $secondsStart;
 my $elapsedMinutes = int($elapsedSeconds/60);
 $elapsedSeconds -= $elapsedMinutes * 60;
 
 # Tell the user anything they should know.
 my $stopStep = $stepper->getStopStep();
 my $upThrough = ($stopStep eq 'cleanup') ? "" :
   "  (through the '$stopStep' step)";
 
 &HgAutomate::verbose(1,
 	"\n *** All done !$upThrough  Elapsed time: ${elapsedMinutes}m${elapsedSeconds}s\n");
 &HgAutomate::verbose(1,
 	" *** Steps were performed in $buildDir\n");
 &HgAutomate::verbose(1, "\n");