629c77052d6b1f7def62cd6cd641b7f383eb8b2c
hiram
  Wed Jul 29 14:54:16 2026 -0700
now archiving versions of NCBI GenBank gene track when updated refs #37958

diff --git src/hg/utils/automation/asmHubNcbiGene.pl src/hg/utils/automation/asmHubNcbiGene.pl
index c6ccac395bc..716ae53ccf3 100755
--- src/hg/utils/automation/asmHubNcbiGene.pl
+++ src/hg/utils/automation/asmHubNcbiGene.pl
@@ -7,105 +7,25 @@
 use AsmHub;
 use File::Basename;
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 4) {
   printf STDERR "usage: asmHubNcbiGene.pl asmId ncbiAsmId asmId.names.tab .../trackData/\n";
   printf STDERR "where asmId is the assembly identifier,\n";
   printf STDERR "and .../trackData/ is the path to the /trackData/ directory.\n";
   printf STDERR "asmId may be equal to ncbiAsmId if it is a GenArk build\n";
   printf STDERR "or asmId might be a default dbName if it is a UCSC style\n";
   printf STDERR "browser build.\n";
   exit 255;
 }
 
-# from Perl Cookbook Recipe 2.17, print out large numbers with comma
-# delimiters:
-sub commify($) {
-    my $text = reverse $_[0];
-    $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;
-    return scalar reverse $text
-}
-
 my $asmId = shift;
 my $ncbiAsmId = shift;
 my $namesFile = shift;
 my $trackDataDir = shift;
 my $ncbiGeneBbi = "$trackDataDir/ncbiGene/$asmId.ncbiGene.bb";
-my $asmType = "refseq";
-
-if ( ! -s $ncbiGeneBbi ) {
-  printf STDERR "ERROR: can not find $asmId.ncbiGene.bb file\n";
-  exit 255;
-}
-
-my @partNames = split('_', $ncbiAsmId);
-my $ftpDirPath = sprintf("%s/%s/%s/%s/%s", $partNames[0],
-   substr($partNames[1],0,3), substr($partNames[1],3,3),
-   substr($partNames[1],6,3), $ncbiAsmId);
-
-$asmType = "genbank" if ($partNames[0] =~ m/GCA/);
-my $totalBases = `/cluster/bin/x86_64/ave -col=2 $trackDataDir/../${asmId}.chrom.sizes | grep "^total" | awk '{printf "%d", \$2}'`;
-chomp $totalBases;
-my $geneStats = `cat $trackDataDir/ncbiGene/${asmId}.ncbiGene.stats.txt | awk '{printf "%d\\n", \$2}' | xargs echo`;
-chomp $geneStats;
-my ($itemCount, $basesCovered) = split('\s+', $geneStats);
-my $percentCoverage = sprintf("%.3f", 100.0 * $basesCovered / $totalBases);
-$itemCount = commify($itemCount);
-$basesCovered = commify($basesCovered);
-$totalBases = commify($totalBases);
-
-my $em = "<em>";
-my $noEm = "</em>";
-my $assemblyDate = `grep -v "^#" $namesFile | cut -f9`;
-chomp $assemblyDate;
-my $ncbiAssemblyId = `grep -v "^#" $namesFile | cut -f10`;
-chomp $ncbiAssemblyId;
-my $organism = `grep -v "^#" $namesFile | cut -f5`;
-chomp $organism;
-
-if ( "${asmType}" eq "refseq" ) {
-
-print <<_EOF_
-<h2>Description</h2>
-<p>
-The NCBI Gene track for the $assemblyDate $em${organism}$noEm/$ncbiAsmId
-genome assembly is constructed from the gff file <b>${ncbiAsmId}_genomic.gff.gz</b>
-supplied with the genome assembly at the FTP location:<br>
-<a href='https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/' target='_blank'>https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/</a>
-</p>
-
-_EOF_
-   ;
-
-} else {
-
-print <<_EOF_
-<h2>Description</h2>
-<p>
-The Gene model track for the $assemblyDate $em${organism}$noEm/$ncbiAsmId
-genome assembly is constructed from the gff file <b>${ncbiAsmId}_genomic.gff.gz</b>
-supplied with the genome assembly at the FTP location:<br>
-<a href='https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/' target='_blank'>https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/</a>
-</p>
-<p>
-The gene models were constructed by the submitter of the assembly to the
-NCBI assembly release system.
-</p>
-
-_EOF_
-    ;
-}
-
-print <<_EOF_
-<h2>Track statistics summary</h2>
-<p>
-<b>Total genome size: </b>$totalBases<br>
-<b>Gene count: </b>$itemCount<br>
-<b>Bases in genes: </b>$basesCovered<br>
-<b>Percent genome coverage: </b>% $percentCoverage<br>
-</p>
+my $statsFile = "$trackDataDir/ncbiGene/${asmId}.ncbiGene.stats.txt";
+my $chromSizes = "$trackDataDir/../${asmId}.chrom.sizes";
 
-_EOF_
-   ;
+print AsmHub::ncbiGeneDescription($ncbiGeneBbi, $statsFile, $chromSizes, $namesFile, $ncbiAsmId);