a3c7c2078036b9b4de1727fe11bb9baac001369e
hiram
  Mon Sep 28 13:32:18 2020 -0700
now with chromAlias and chromSizes in genomes.txt refs #23891

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index 0222ee0..0bab760 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -53,79 +53,91 @@
 
 my $buildDone = 0;
 my $orderKey = 0;
 foreach my $asmId (@orderList) {
   ++$orderKey;
   my ($gcPrefix, $accession, undef) = split('_', $asmId);
   my $accessionId = sprintf("%s_%s", $gcPrefix, $accession);
   my $accessionDir = substr($asmId, 0 ,3);
   $accessionDir .= "/" . substr($asmId, 4 ,3);
   $accessionDir .= "/" . substr($asmId, 7 ,3);
   $accessionDir .= "/" . substr($asmId, 10 ,3);
   my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
   if ($gcPrefix eq "GCA") {
      $buildDir = "/hive/data/genomes/asmHubs/genbankBuild/$accessionDir/$asmId";
   }
+  if ( ! -s "${buildDir}/${asmId}.chrom.sizes" ) {
+    printf STDERR "# ERROR: missing ${asmId}.chrom.sizes in\n# ${buildDir}\n";
+    next;
+  }
+  if ( ! -s "${buildDir}/${asmId}.chromAlias.txt" ) {
+    printf STDERR "# ERROR: missing ${asmId}.chromAlias.txt in\n# ${buildDir}\n";
+    next;
+  }
   my $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
   my $trackDb = "$buildDir/$asmId.trackDb.txt";
   if ( ! -s "${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;
 
   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;
   $tenK = $bigChrom if ($tenK > $bigChrom);
   my $defPos="${chrName}:${oneThird}-${tenK}";
   if ( -s "$asmId/defaultPos.txt" ) {
     $defPos=`cat "$asmId/defaultPos.txt"`;
     chomp $defPos;
   }
   printf "defaultPos %s\n", $defPos;
   printf "orderKey %d\n", $buildDone;
   printf "scientificName %s\n", $descr;
   printf "htmlPath ../%s/%s/html/%s.description.html\n", $accessionDir, $accessionId, $asmId;
   printf "\n";
   my $localGenomesFile = "$buildDir/${asmId}.genomes.txt";
   my $localOrderKey;
   open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
   printf GF "genome %s\n", $accessionId;
   printf GF "trackDb trackDb.txt\n";
   printf GF "groups groups.txt\n";
   printf GF "description %s\n", $orgName;
   printf GF "twoBitPath %s.2bit\n", $accessionId;
+  printf GF "chromSizes %s.chrom.sizes.txt\n", $accessionId;
+  printf GF "chromAlias %s.chromAlias.txt\n", $accessionId;
   printf GF "organism %s\n", $descr;
   printf GF "defaultPos %s\n", $defPos;
   printf GF "orderKey %d\n", $localOrderKey++;
   printf GF "scientificName %s\n", $descr;
   printf GF "htmlPath html/%s.description.html\n", $asmId;
   close (GF);
   my $localHubTxt = "$buildDir/${asmId}.hub.txt";
   open (HT, ">$localHubTxt") or die "can not write to $localHubTxt";
   printf HT "hub %s genome assembly\n", $accessionId;
   printf HT "shortLabel %s\n", $orgName;
   printf HT "longLabel %s/%s/%s genome assembly\n", $orgName, $descr, $asmId;
   printf HT "genomesFile genomes.txt\n";
   printf HT "email hclawson\@ucsc.edu\n";
   printf HT "descriptionUrl html/%s.description.html\n", $asmId;
   close (HT);