2bcf12483a026f2f164ad1748334d0dec72a26de
hiram
  Mon Jan 25 15:21:25 2021 -0800
can use better common name when available for genomes.txt description refs #23891

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index 0bab760..d88f9ee 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -78,30 +78,33 @@
   if ( ! -s "${trackDb}" ) {
     printf STDERR "# %03d not built yet: %s\n", $orderKey, $asmId;
     printf STDERR "# '%s'\n", $trackDb;
     next;
   }
   if ( ! -s "${asmReport}" ) {
     printf STDERR "# %03d missing assembly_report: %s\n", $orderKey, $asmId;
     next;
   }
   ++$buildDone;
 printf STDERR "# %03d genomes.txt %s/%s\n", $buildDone, $accessionDir, $accessionId;
   my $descr=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.*organism name: *##i; s# (.*\$##;'`;
   chomp $descr;
   my $orgName=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.* name: .* (##; s#).*##;'`;
   chomp $orgName;
+  if (defined($commonName{$asmId})) {
+     $orgName = $commonName{$asmId};
+  }
 
   printf "genome %s\n", $accessionId;
   printf "trackDb ../%s/%s/trackDb.txt\n", $accessionDir, $accessionId;
   printf "groups groups.txt\n";
   printf "description %s\n", $orgName;
   printf "twoBitPath ../%s/%s/%s.2bit\n", $accessionDir, $accessionId, $accessionId;
   printf "chromSizes ../%s/%s/%s.chrom.sizes.txt\n", $accessionDir, $accessionId, $accessionId;
   printf "chromAlias ../%s/%s/%s.chromAlias.txt\n", $accessionDir, $accessionId, $accessionId;
   printf "organism %s\n", $descr;
   my $chrName=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$1}'`;
   chomp $chrName;
   my $bigChrom=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$NF}'`;
   chomp $bigChrom;
   my $oneThird = int($bigChrom/3);
   my $tenK = $oneThird + 10000;