da977cb10ba717d64216de2cbeeb9948c9c78714
hiram
  Wed Mar 2 16:33:41 2022 -0800
adding crisprAll as an asmHub track no redmine

diff --git src/hg/utils/automation/asmHubXenoRefGene.pl src/hg/utils/automation/asmHubXenoRefGene.pl
index 076679b..8d8a6f3 100755
--- src/hg/utils/automation/asmHubXenoRefGene.pl
+++ src/hg/utils/automation/asmHubXenoRefGene.pl
@@ -16,43 +16,36 @@
   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 $namesFile = shift;
 my $trackDataDir = shift;
 my $xenoRefGeneBbi = "$trackDataDir/xenoRefGene/$asmId.xenoRefGene.bb";
-my $asmType = "refseq";
 
 if ( ! -s $xenoRefGeneBbi ) {
   printf STDERR "ERROR: can not find $asmId.xenoRefGene.bb file\n";
   exit 255;
 }
 
-my @partNames = split('_', $asmId);
-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), $asmId);
-
-$asmType = "genbank" if ($partNames[0] =~ m/GCA/);
 my $totalBases = `ave -col=2 $trackDataDir/../${asmId}.chrom.sizes | grep "^total" | awk '{printf "%d", \$2}'`;
 chomp $totalBases;
 my $geneStats = `cat $trackDataDir/xenoRefGene/${asmId}.xenoRefGene.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`;