57a2bac4726971e593dc92902803e55667782882
hiram
  Mon May 22 13:34:49 2023 -0700
adding Ensembl relations in chromAlias and new extended ensGene track to host Rapid Release ensGene refs #31332

diff --git src/hg/utils/automation/asmHubChromAlias.pl src/hg/utils/automation/asmHubChromAlias.pl
index 524146a..b910503 100755
--- src/hg/utils/automation/asmHubChromAlias.pl
+++ src/hg/utils/automation/asmHubChromAlias.pl
@@ -174,30 +174,51 @@
     chomp $line;
     my ($native, $alias) = split('\s+', $line);
     if (!defined($sequenceSizes{$native})) {
        printf STDERR "ERROR: processing customNames.tsv given native name\n";
        printf STDERR " '%s' that does not exist (alias: %s)\n", $native, $alias;
        exit 255;
     }
     $customName{$native} = $alias;
     ++$customNameCount;
     addAlias("custom", $alias, $native);
   }
   close (FH);
   printf STDERR "# read %d custom alias names from customNames.tsv\n", $customNameCount;
 }
 
+my %ensemblName;	# key is native sequence name, value is a ensembl alias
+my $ensemblNameCount = 0;
+
+if ( -s "ensemblNames.tsv" ) {
+  open (FH, "<ensemblNames.tsv") or die "can not read ensemblNames.tsv";
+  while (my $line = <FH>) {
+    chomp $line;
+    my ($native, $alias) = split('\s+', $line);
+    if (!defined($sequenceSizes{$native})) {
+       printf STDERR "ERROR: processing ensemblNames.tsv given native name\n";
+       printf STDERR " '%s' that does not exist (alias: %s)\n", $native, $alias;
+       exit 255;
+    }
+    $ensemblName{$native} = $alias;
+    ++$ensemblNameCount;
+    addAlias("ensembl", $alias, $native);
+  }
+  close (FH);
+  printf STDERR "# read %d ensembl alias names from ensemblNames.tsv\n", $ensemblNameCount;
+}
+
 my $nameCount = 0;
 my %ncbiToUcsc;	# key is NCBI sequence name, value is 'chr' UCSC chromosome name
 my %ucscToNcbi;	# key is 'chr' UCSC name, value is NCBI sequence name
 open (FH, "cat ../../sequence/*.names|") or die "can not cat ../../sequence/*.names";
 while (my $line = <FH>) {
   chomp $line;
   my ($ucscName, $seqName) = split('\s+', $line);
   $ncbiToUcsc{$seqName} = $ucscName;
   $ucscToNcbi{$ucscName} = $seqName;
   ++$nameCount;
   $ucscNames = 1 if (defined($sequenceSizes{$ucscName}));
   if ($isRefSeq) {
     $ucscToRefSeq{$ucscName} = $seqName;
   } else {
     $ucscToGenbank{$ucscName} = $seqName;