452b689cab327a20bb7ac506eaf89a3f69d23feb
hiram
  Tue Jan 17 08:23:41 2023 -0800
invertebrates has become invertebrate and master.run.list has changed columns no redmine

diff --git src/hg/gar/garTable.pl src/hg/gar/garTable.pl
index 247d28b..a803556 100755
--- src/hg/gar/garTable.pl
+++ src/hg/gar/garTable.pl
@@ -1,1431 +1,1430 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 
 # 1. reading iucnToNcbiEquivalent.txt to get ncbiToIucnNames hash
 # 2. reading iucn/IUCN.CR.txt
 # 3. reading iucn/IUCN.EN.txt
 # 4. reading iucn/IUCN.VU.txt
 # 5. reading iucn/links.csv
 # 6. reading asmId.sciName.commonName to get better common names
 # 7. reading accumulateMetaInfo.tsv to get better common names
 # 8. reading ../../../sizes/asmId.sciName.commonName.date.tsv
 # 9. reading assembly_summary_genbank.txt and assembly_summary_refseq.txt
              # to get asmId and scientific names for all assemblies
 # 10. reading asmId.suppressed.list
 # 11. reading asmId.date.taxId.asmSubmitter.tsv
 # 12. reading asmId.country.date.by.tsv
 # 13. now in a perClade loop, reading each all.*.clade.today listings
       # to get all refseq and genbank assemblies
 # 14. during that loop, it may use the sizes chromInfo and the n50.txt
       # files from
 # /hive/data/outside/ncbi/genomes/sizes/gcX/d0/d1/d2/asmId.chromInfo.txt";
 
 ###############################################################################
 # 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
 }
 ###############################################################################
 
 ###############################################################################
 # obtain assembly size and sequence count from chromInfo file
 sub sizeUpChromInfo($) {
   my ($ciFile) = @_;
   my $sizeCount=`ave -col=2 "$ciFile" | egrep -w "count|total" | awk '{printf "%d ", \$NF}'`;
   chomp $sizeCount;
   my ($count, $size, undef) = split('\s+', $sizeCount, 3);
   return ($size, $count);
 }
 ###############################################################################
 
 ###############################################################################
 # read an N50.txt output file from n50.pl to extract the size and count
 sub readN50($) {
   my ($n50File) = @_;
   my $size = 0;
   my $count = 0;
   open (TF, "grep -v '^#' $n50File|") or die "can not read $n50File";
   while (my $line = <TF>) {
     chomp $line;
     my @a = split('\s+', $line);
     last if ($size > $a[0]);
     if ($a[1] ne "one") {
       $size = $a[3];
       $count = $a[1];
     }
   }
   close (TF);
   return ($size, $count);
 }
 ###############################################################################
 
 ###############################################################################
 # given a number, return reduced significant digits for giga, mega, kilo or none
 sub gmk($) {
   my ($n) = @_;
   return sprintf("%d", $n) if ($n < 1000);
   my $m = $n/1000;
   return sprintf("%.2fK", $m) if ($m < 1000);
   $m = $n/1000000;
   return sprintf("%.2fM", $m) if ($m < 1000);
   $m = $n/1000000000;
   return sprintf("%.3fG", $m);
 }
 ###############################################################################
 
 ###############################################################################
 # output a table cell for an N50 measurement
 sub n50Cell($$$) {
   my ($size, $count, $fh) = @_;
   if ($size > 0) {
     printf "<td style='display:none; text-align:right;' sorttable_customkey='%d'>%s&nbsp;(%s)</td>", $size, gmk($size), commify($count);
     printf $fh "\t%d (%d)", $size, $count;	# output to clade.tableData.txt
   } else {
     printf "<td style='display:none;'>&nbsp;</td>";
     printf $fh "\tn/a (n/a)";	# output to clade.tableData.txt
   }
 }
 ###############################################################################
 
-my @clades = qw( primates mammals birds fish vertebrate invertebrates plants fungi );
+my @clades = qw( primates mammals birds fish vertebrate invertebrate plants fungi );
 
 # to help weed out some of the noise
 # key is clade, value is minimal size to count as a whole genome
 # these are actually pretty low to allow in some alternate haplotype
 # assemblies that don't seem to be the whole assembly.
 # The assemblies are also filtered by NCBI status 'full/partial' to only
 # allow in the 'full' genomes meaning representation of the whole genome
 my %minimalGenomeSize = (
   primates => 1000000000,
   mammals => 20000000,
   birds => 200000000,
   fish => 100000,
   vertebrate => 4000000,
-  invertebrates => 10000,
+  invertebrate => 10000,
   plants => 100000,
   fungi => 50000,
 );
 
 #########################################################################
 ## read in list of current GenArk assemblies
 
 my %genArkAsm;	# key is asmId, value is string with:
 my %genArkClade;	# key is asmId, value is clade
 my %genArkCladeProfile;	# key is clade, value is count
 my %genArkSciName;	# key is asmId, value is sciName
 my %genArkComName;	# key is asmId, value is sciName
 
 # accession<tab>assembly<tab>scientific name<tab>common name<tab>taxonId<tab>clade
 
 my $genArkCount = 0;
 printf STDERR "# reading UCSC_GI.assemblyHubList.txt\n";
 open (FH, "<UCSC_GI.assemblyHubList.txt") or die "can not read UCSC_GI.assemblyHubList.txt";
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp $line;
   my ($accession, $assembly, $sciName, $commonName, $taxonId, $gClade) = split('\t', $line);
   my $asmId = sprintf("%s_%s", $accession, $assembly);
   die "ERROR: duplicate accession from UCSC_GI.assemblyHubList.txt" if (defined($genArkAsm{$asmId}));
   $genArkAsm{$asmId} = sprintf("%s\t%s\t%s\t%s\t%s", $accession, $assembly, $sciName, $commonName, $taxonId);
   $gClade =~ s/\(L\)//;	# remove the 'legacy' tag
-  $gClade = "invertebrates" if ($gClade =~ m/invertebrate/);
   $genArkClade{$asmId} = $gClade;
   ++$genArkCladeProfile{$gClade};
   ++$genArkCount;
 }
 close (FH);
 
 # accession     assembly        scientific name common name     taxonId
 # GCA_000001905.1 Loxafr3.0       Loxodonta africana      African savanna elephant (2009 genbank) 9785
 
 printf STDERR "# have %s assemblies from GenArk UCSC_GI.assemblyHubList.txt\n", commify($genArkCount);
 printf STDERR "# genArk clade profile:\n";
 foreach my $gClade (sort keys %genArkCladeProfile) {
   printf STDERR "# %6d\t%s\n", $genArkCladeProfile{$gClade}, $gClade;
 }
 
 my $rrCount = 0;
 my %rrGcaGcfList;	# key is asmId, value is UCSC db name
 open (FH, "<rr.GCF.GCA.list") or die "can not read rr.GCF.GCA.list";
 while (my $line = <FH>) {
   chomp $line;
   my ($ucscDb, $asmId) = split('\s+', $line);
   $rrGcaGcfList{$asmId} = $ucscDb;
   ++$rrCount;
 }
 close (FH);
 
 printf STDERR "# have %d assemblies with RR equivalent databases\n", $rrCount;
 printf STDERR "# therefore, should be a total of %s existing browsers\n", commify($rrCount+$genArkCount-$genArkCladeProfile{'viral'}-$genArkCladeProfile{'bacteria'});
 printf STDERR "# %s + %s - %s - %s = %s\n", commify($genArkCount), commify($rrCount), commify($genArkCladeProfile{'viral'}), commify($genArkCladeProfile{'bacteria'}), commify($rrCount+$genArkCount-$genArkCladeProfile{'viral'}-$genArkCladeProfile{'bacteria'});
 
 # establish a name equivalence for some NCBI three word scientific names
 # to IUCN two word scientific names
 
 my %ncbiToIucnNames;	# key is NCBI name (one), value is IUCN name (many)
 # for example:
 # Giraffa camelopardalis antiquorum -> Giraffa camelopardalis
 # Giraffa camelopardalis rothschildi -> Giraffa camelopardalis
 
 printf STDERR "### reading iucnToNcbiEquivalent.txt\n";
 open (FH, "<../iucnToNcbiEquivalent.txt") or die "can not read iucnToNcbiEquivalent.txt";
 while (my $line = <FH>) {
   chomp $line;
   my ($ncbiName, $iucnName) = split('\t', $line);
   $ncbiToIucnNames{$ncbiName} = $iucnName;
 }
 close (FH);
 
 my $criticalColor = "#ff0000";
 my $endangeredColor = "#dd6600";
 my $vulnerableColor = "#663300";
 $criticalColor = "#ee3333";
 $endangeredColor = "#333388";
 $vulnerableColor = "#88aaaa";
 my %statusColors = (
   "CR" => $criticalColor,
   "EN" => $endangeredColor,
   "VU" => $vulnerableColor,
 );
 
 my %iucnCR;	# key is scientific name, value is 1 == Critically Endangered
 my %iucnEN;	# key is scientific name, value is 1 == Endangered
 my %iucnVU;	# key is scientific name, value is 1 == Vulnerable
 
 my %iucnSciNames;	# key is scientific name, value is IUCN code CR EN VU
 
 my $iucnSpeciesCount = 0;
 my $iucnCount = 0;
 printf STDERR "### reading iucn/IUCN.CR.txt\n";
 open (FH, "<../iucn/IUCN.CR.txt") or die "can not read iucn/IUCN.CR.txt";
 while (my $sName = <FH>) {
   chomp $sName;
   $iucnCR{$sName} = 1;
   ++$iucnCount;
   $iucnSciNames{$sName} = "CR";
 }
 close (FH);
 printf STDERR "# IUCN Critical %s\n", commify($iucnCount);
 $iucnSpeciesCount += $iucnCount;
 
 $iucnCount = 0;
 printf STDERR "### reading iucn/IUCN.EN.txt\n";
 open (FH, "<../iucn/IUCN.EN.txt") or die "can not read iucn/IUCN.EN.txt";
 while (my $sName = <FH>) {
   chomp $sName;
   $iucnEN{$sName} = 1;
   ++$iucnCount;
   die "ERROR: duplicate sciName in IUCN CR and EN listings" if (defined($iucnCR{$sName}));
   $iucnSciNames{$sName} = "EN";
 }
 close (FH);
 printf STDERR "# IUCN Endangered %s\n", commify($iucnCount);
 $iucnSpeciesCount += $iucnCount;
 
 $iucnCount = 0;
 printf STDERR "### reading iucn/IUCN.VU.txt\n";
 open (FH, "<../iucn/IUCN.VU.txt") or die "can not read iucn/IUCN.VU.txt";
 while (my $sName = <FH>) {
   chomp $sName;
   $iucnVU{$sName} = 1;
   ++$iucnCount;
   $iucnSciNames{$sName} = "VU";
   die "ERROR: duplicate sciName in IUCN CR and VU listings" if (defined($iucnCR{$sName}));
   die "ERROR: duplicate sciName in IUCN EN and VU listings" if (defined($iucnEN{$sName}));
 }
 close (FH);
 printf STDERR "# IUCN Vulnerable %s\n", commify($iucnCount);
 $iucnSpeciesCount += $iucnCount;
 
 my %iucnLink;	# key is sciName, value is the two id numbers 123/456
 		# to make a link: https://www.iucnredlist.org/species/123/456
 # get the id numbers from iucn to make links to IUCN
 printf STDERR "### reading iucn/links.csv\n";
 open (FH, "<../iucn/links.csv") or die "can not read iucn/links.csv";
 while (my $line = <FH>) {
   chomp $line;
   my ($n2, $n1, $sName) = split(',', $line);
   $iucnLink{$sName} = sprintf("%d/%d", $n1, $n2);
 }
 close (FH);
 
 my $comNameCount = 0;
 my %ncbiCommonName;	# key is asmId, value is common name from NCBI assembly_report
 my %ncbiDate;	# key is asmId, value is assembly submission date from NCBI assembly_report
 
 #  common names from genArk hubs, better common name when available
 my $hubComNames = 0;
 my %sciName;	# key is asmId, value is scientific name
 my %comName;	# key is asmId, value is common name
 printf STDERR "### reading asmId.sciName.commonName\n";
 open (FH, "<asmId.sciName.commonName") or die "can not read asmId.sciName.commonName";
 while (my $line = <FH>) {
   chomp $line;
   my ($id, $sci, $com) = split('\t', $line);
   $sci =~ s/_/ /g;
   if (defined($sciName{$id})) {
     die "ERROR: duplicate asmId sciName: $id '$sci' '$sciName{$id}'";
   }
   $sciName{$id} = $sci;
   $comName{$id} = $com;
   ++$hubComNames;
 }
 close (FH);
 
 printf STDERR "# common names from GenArk hubs: %s\n", commify($hubComNames);
 
 my $genArkCatchup = 0;
 my $genArkDone = 0;
 ### catch up for any missed genArk hubs
 # accession<tab>assembly<tab>scientific name<tab>common name<tab>taxonId
 foreach my $asmIdKey (sort keys %genArkAsm) {
   if (defined($sciName{$asmIdKey})) {
     ++$genArkDone;
     next;
   }
   if (defined($comName{$asmIdKey})) {
     ++$genArkDone;
     next;
   }
   my @a = split('\t', $genArkAsm{$asmIdKey});
   $a[2] =~ s/_/ /g;
   $sciName{$asmIdKey} = $a[2];
   $comName{$asmIdKey} = $a[3];
   ++$genArkCatchup;
 }
 
 printf STDERR "# %d genArk hubs from hgdownload list already done\n", $genArkDone;
 printf STDERR "# catch up %d genArk hubs from hgdownload list\n", $genArkCatchup;
 
 my %metaInfo;	# key is asmId, value is a tsv string of numbers for:
                 # asmSize asmContigCount n50Size n50Count n50ContigSize
 		# n50ContigCount n50ScaffoldSize n50ScaffoldCount
 my %newMetaInfo;	# accumulate new metaInfo to add to end of this file
 
 if ( -s "../accumulateMetaInfo.tsv" ) {
   printf STDERR "# reading ../accumulateMetaInfo.tsv\n";
   open (FH, "<../accumulateMetaInfo.tsv") or die "can not read ../accumulateMetaInfo.tsv";
   while (my $line = <FH>) {
     chomp $line;
     my ($asmId, $metaData) = split('\t', $line, 2);
     die "ERROR: duplicate metaInfo{$asmId}" if (defined($metaInfo{$asmId}));
     $metaInfo{$asmId} = $metaData;
   }
   close (FH);
 }
 
 my $noDateFromSize = 0;
 my $earliestDate = 22001231;
 my $latestDate = 19000101;
 printf STDERR "### reading asmId.sciName.comonName.date.tsv\n";
 open (FH, "<../asmId.sciName.commonName.date.tsv") or die "can not read ../asmId.sciName.commonName.date.tsv";
 while (my $line = <FH>) {
   chomp $line;
   my @a = split('\t', $line);
   next if ($a[0] !~ m/^GC/);
   $a[0] =~ s/__/_/g;
   ++$comNameCount;
   $ncbiCommonName{$a[0]} = $a[2];
   if (defined($a[3]) && ($a[3] =~ m/^[12][0-9][0-9][0-9]-[0-9]+-[0-9]+$/) ) {
      my @b = split('-', $a[3]);
      $ncbiDate{$a[0]} = sprintf("%04d%02d%02d", $b[0], $b[1], $b[2]);
      $earliestDate = $ncbiDate{$a[0]} if ($ncbiDate{$a[0]} < $earliestDate);
      $latestDate = $ncbiDate{$a[0]} if ($latestDate < $ncbiDate{$a[0]});
   } else {
      $ncbiDate{$a[0]} = 19720101;
      ++$noDateFromSize;
      if (defined($a[3])) {
        printf STDERR "# no date '%s' for %s'\n", $a[3], $a[0] if ($noDateFromSize < 5);
      } else {
        printf STDERR "# no date 'undef' for %s'\n", $a[0] if ($noDateFromSize < 5);
      }
   }
 }
 close (FH);
 printf STDERR "# comNameCount %s from ../../../sizes/asmId.sciName.commonName.date.tsv\n", commify($comNameCount);
 printf STDERR "# dates from %s to %s, no dates: %d\n", $earliestDate, $latestDate, $noDateFromSize;;
 
 my %sciNameCount;	# key is scientific name, value is count of assemblies
 			# from NCBI assembly_summary .txt files
 my %sciNames;	# key is asmId, value is scientific name
 my %sciNameAsmList;	# key is scientific name, value is pointer to array
 			# which is a list of assemblies on this sciName
 
 # goodToGo will be the master asmId list for output
 my %goodToGoSpecies;	# key is scientific name, value is asmId selected
 my %goodToGo;	# key is asmId, value is iucn status code CR EN VU
 my %goodToGoDate;	# key is sciName, value is date YYYYMMDD for selected
 			# assembly
 # choices in order when duplicate species:
 # GCA assembly
 # newer GCA assembly
 # GCF assembly
 # newer GCF assembly
 
 my $ncbiTotalAssemblies = 0;
 my $ncbiUniqueSpecies = 0;
 my $highestSpeciesCount = 0;
 my $highestCountName = "";
 
 my $countingGoodToGo = 0;
 my $goodToGoReplaced = 0;
 my $warningNoDate = 0;
 
 my %skipPartialGenome;	# key is asmId, value is sciName for 'partial' status
 
 my $genomeReports = "/hive/data/outside/ncbi/genomes/reports";
 
 # obtain scientific name and asmId from assembly_summary files
 printf STDERR "### reading genbank and refseq assembly_summary\n";
 open (FH, "grep -v '^#' $genomeReports/assembly_summary_genbank.txt $genomeReports/assembly_summary_refseq.txt $genomeReports/assembly_summary_genbank_historical.txt $genomeReports/assembly_summary_refseq_historical.txt|cut -f8,14,20|") or die "can not read the assembly_summary files";
 while (my $line = <FH>) {
   chomp $line;
   # asmId will be derived from the ftpPath
   my ($sName, $fullPartial, $asmId) = split('\t', $line);
   # most interesting, skipping these partial assemblies ends up with more
   # in the final result ?
   $asmId =~ s#.*/##;
   next if ($asmId =~ m/^na$/);
   # something wrong with these two
   next if ($asmId =~ m/GCA_900609255.1|GCA_900609265.1/);
   if ($fullPartial =~ m/partial/i) {        # skip partial assemblies
     $skipPartialGenome{$asmId} = $sName;
     next;
   }
   ++$sciNameCount{$sName};
   $sciNames{$asmId} = $sName;
   if (!defined($sciNameAsmList{$sName})) {
     my @a;
     $sciNameAsmList{$sName} = \@a;
   }
   my $sPtr = $sciNameAsmList{$sName};
   push (@$sPtr, $asmId);	# maintain list of asmIds for this sciName
   ++$ncbiTotalAssemblies;
   ++$ncbiUniqueSpecies if (1 == $sciNameCount{$sName});
   if ($sciNameCount{$sName} > $highestSpeciesCount) {
     $highestSpeciesCount = $sciNameCount{$sName};
     $highestCountName = $sName;
   }
   # only selecting assemblies if IUCN classification exists
   my $iucnSciName = $sName;	# check name equivalence
  $iucnSciName = $ncbiToIucnNames{$sName} if (defined($ncbiToIucnNames{$sName}));
 #### XXX ### let's try everything instead of just those with IUCN class
   if ( 1 == 1 || defined($iucnSciNames{$iucnSciName})) {
     if (defined($goodToGoSpecies{$sName})) {	# already seen
       my $prevGC = $goodToGoSpecies{$sName};	# see if it should be override
       if ($prevGC =~ m/^GCA/) {
          if ($asmId =~ m/^GCF/) {	# GCF overrides GCA
            $goodToGoSpecies{$sName} = $asmId;
            delete $goodToGo{$prevGC};
            ++$goodToGoReplaced;
            $goodToGo{$asmId} = $iucnSciNames{$iucnSciName};
            if (defined($ncbiDate{$asmId})) {
              $goodToGoDate{$sName} = $ncbiDate{$asmId};
            } else {
 #        printf STDERR "# 0 warning: no ncbiDate for $asmId $sName '$line'\n";
              ++$warningNoDate;
              $goodToGoDate{$sName} = 19720101;
            }
          } else {	# another GCA, check dates
            if (defined($ncbiDate{$asmId})) {
              if ($ncbiDate{$asmId} > $goodToGoDate{$sName}) { # newer
                delete $goodToGo{$prevGC};
                ++$goodToGoReplaced;
                $goodToGoSpecies{$sName} = $asmId;
                $goodToGo{$asmId} = $iucnSciNames{$iucnSciName};
                $goodToGoDate{$sName} = $ncbiDate{$asmId};
              } else {
              }
            } else {	# no date, no replace
 #       printf STDERR "# 1 warning: no ncbiDate for $asmId $sName '$line'\n";
              ++$warningNoDate;
            }
          }
       } elsif ($asmId =~ m/^GCF/) {	# a second GCF
         if (defined($ncbiDate{$asmId})) {
           if ($ncbiDate{$asmId} > $goodToGoDate{$sName}) { # newer
              delete $goodToGo{$prevGC};
              ++$goodToGoReplaced;
              $goodToGoSpecies{$sName} = $asmId;
              $goodToGo{$asmId} = $iucnSciNames{$iucnSciName};
              $goodToGoDate{$sName} = $ncbiDate{$asmId};
           } else {
           }
         } else {	# no date, no replace
 #        printf STDERR "# 2 warning: no ncbiDate for $asmId $sName '$line'\n";
              ++$warningNoDate;
         }
       }
     } else {	# first time, take this assembly
       ++$countingGoodToGo;
       $goodToGoSpecies{$sName} = $asmId;
       $goodToGo{$asmId} = $iucnSciNames{$iucnSciName};
       if (defined($ncbiDate{$asmId})) {
         $goodToGoDate{$sName} = $ncbiDate{$asmId};
       } else {
 #      printf STDERR "# 3 warning: no ncbiDate for $asmId $sName '$line'\n";
              ++$warningNoDate;
         $goodToGoDate{$sName} = 19720101;
       }
     }
   } 	#	if (defined($iucnSciNames{$iucnSciName}))
 }	#	while (my $line = <FH>) reading the assembly_summary files
 close (FH);
 
 printf STDERR "# countedGoodToGo: %d, replaced: %d, noDate: %d\n", $countingGoodToGo, $goodToGoReplaced, $warningNoDate;
 printf STDERR "# have %s NCBI assemblies, %s unique NCBI species\n", commify($ncbiTotalAssemblies), commify($ncbiUniqueSpecies);
 printf STDERR "#\thighest species count %s : '%s'\n", commify($highestSpeciesCount), $highestCountName;
 
 my %gcxCountry;	# key is asmId, value is collection location
 my %gcxDate;	# key is asmId, value is collection date
 my %gcxSubmitter;	# key is asmId, value is collected by
 my %asmSuppressed;	# key is asmId, value is 1 meaning suppressed
 
 printf STDERR "### reading asmId.suppressed.list\n";
 open (FH, "<asmId.suppressed.list") or die "can not read asmId.suppressed.list";
 while (my $id = <FH>) {
   chomp $id;
   next if (defined($genArkAsm{$id}) || defined($rrGcaGcfList{$id}));
   $asmSuppressed{$id} = 1;
 }
 close (FH);
 
 my %asmDate;	# key is asmId, value is date of assembly
 my %asmSubmitter;	# key is asmId, value is name of assembly submitter
 my %asmTaxId;	# key is asmId, value is taxId of species
 
 my $asmIdCount = 0;
 printf STDERR "### reading ../asmId.date.taxId.asmSubmitter.tsv\n";
 open (FH, "<../asmId.date.taxId.asmSubmitter.tsv") or die "can not read a../smId.date.taxId.asmSubmitter.tsv";
 while (my $line = <FH>) {
   chomp $line;
   my ($id, $da, $tid, $asmS) = split('\t', $line);
   $id =~ s/__/_/g;
   $da = "&nbsp;" if ($da =~ m#n/a#);
   $tid = "&nbsp;" if ($tid =~ m#n/a#);
   $asmS = "&nbsp;" if ($asmS =~ m#n/a#);
   $asmDate{$id} = $da;
   $asmTaxId{$id} = $tid;
   $asmSubmitter{$id} = $asmS;
   ++$asmIdCount;
 }
 close (FH);
 printf STDERR "# asmId count: %s from asmId.date.taxId.asmSubmitter.tsv\n", commify($asmIdCount);
 
 $asmIdCount = 0;
 printf STDERR "### reading ../asmId.country.date.by.tsv\n";
 open (FH, "<../asmId.country.date.by.tsv") or die "can not read ../asmId.country.date.by.tsv";
 while (my $line = <FH>) {
   chomp $line;
   my ($id, $country, $collectDate, $submitter) = split('\t', $line);
   $id =~ s/__/_/g;
   if (defined($gcxCountry{$id})) {
     die "ERROR: duplicate asmId data $id '$country' '$gcxCountry{$id}'";
   }
   printf STDERR "# undefined collectDate for $id" if (!defined($collectDate));
   printf STDERR "# undefined submitter for $id" if (!defined($submitter));
   $country =~ s/"//g;
   $collectDate =~ s/"//g;
   $submitter =~ s/"//g;
   $gcxCountry{$id} = $country;
   $gcxDate{$id} = $collectDate;
   $gcxSubmitter{$id} = $submitter;
   ++$asmIdCount;
 }
 close (FH);
 printf STDERR "# asmId count: %s from asmId.country.date.by.tsv\n", commify($asmIdCount);
 
 my %asmReportData;	# key is asmId, value is tsv string for:
 #     sciName commonName bioSample bioProject taxId asmDate
 # obtained from scanning all the assembly report files
 open (FH, "<../asmReport.data.tsv") or die "can not read ../asmReport.data.tsv";
 while (my $line = <FH>) {
   chomp $line;
   my ($id, $rest) = split('\t', $line, 2);
   $asmReportData{$id} = $rest;
 }
 close (FH);
 
 ### This cladeToGo set of lists is the main driver of the table
 ### An assembly needs to be in this set in order to get into the table
 my %cladeToGo;	# key is clade name, value is array pointer for asmId list
 my $totalGoodToGo = 0;
 my %cladeCounts;	# key is clade name, value is count of assemblies used
 
 my $maxDupAsm = 0;
 my %ncbiSpeciesRecorded;	# key is NCBI sciName, value is count of those
 my $ncbiSpeciesUsed = 0;	# a unique count of NCBI sciName
 my %iucnSpeciesRecorded;	# key is IUCN sciName, value is count of those
 my $iucnSpeciesUsed = 0;	# a unique count of IUCN sciName
 
 my $sciNameDisplayLimit = 5;    # do not display more than 5 instances
 
 my $checkedAsmIds = 0;
 my $acceptedAsmIds = 0;
 my $notInGoodToGo = 0;
 my %alreadyDone;	# key is asmId, value = 1 indicates already done
 my %underSized;		# key is clade, value is count of underSized
 
 my $NA = "/hive/data/outside/ncbi/genomes/reports/newAsm";
 
 my $examinedAsmId = 0;
 my $shouldBeGenArk = 0;
 my $shouldBeUcsc = 0;
 my %usedGenArk;	# key is asmId, value is count seen in *.today files
 my $genArkTooManySpecies = 0;
 my $countingUsedGenArk = 0;
 my $prevUsedGenArk = 0;
 
 foreach my $clade (@clades) {
   my $cladeCount = 0;
   my $goodToGoCount = 0;
   my $refSeq = "${NA}/all.refseq.${clade}.today";
   my $genBank = "${NA}/all.genbank.${clade}.today";
   my $asmHubTsv = "~/kent/src/hg/makeDb/doc/${clade}AsmHub/${clade}.orderList.tsv";
-  if ($clade eq "invertebrates") {
+  if ($clade eq "invertebrate") {
     $asmHubTsv = "~/kent/src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv";
   }
   open (FH, "cut -f1 ${refSeq} ${genBank} ${asmHubTsv}|sort -u|") or die "can not read $refSeq or $genBank or $asmHubTsv";
   while (my $asmId = <FH>) {
      chomp $asmId;
      ++$examinedAsmId;
      $asmId =~ s/\.]/_/g;
      $asmId =~ s/\:/_/g;
      $asmId =~ s/\%/_/g;
      $asmId =~ s/\+/_/g;
      $asmId =~ s/\//_/g;
      $asmId =~ s/\#/_/g;
 #      $asmId =~ s/[.:%+/#]/_/g;
      $asmId =~ s/[()]//g;
      $asmId =~ s/__/_/g;
      ++$shouldBeGenArk if (defined($genArkAsm{$asmId}));
      ++$shouldBeUcsc if (defined($rrGcaGcfList{$asmId}));
      if (defined ($skipPartialGenome{$asmId})) {
        next if (!defined($genArkAsm{$asmId}) && !defined($rrGcaGcfList{$asmId}));
      }
      if (defined ($asmSuppressed{$asmId})) {
        next if (!defined($genArkAsm{$asmId}) && !defined($rrGcaGcfList{$asmId}));
      }
      next if (defined ($alreadyDone{$asmId}));
      # something wrong with these two
 # GCA_900609255.1_Draft_mitochondrial_genome_of_wild_rice_W1683
 # GCA_900609265.1_Draft_mitochondrial_genome_of_wild_rice_W1679
      next if ($asmId =~ m/GCA_900609255.1|GCA_900609265.1/);
      # verify this asmId will pass the asmSize limit
      if (defined($metaInfo{$asmId})) {
       my ($asmSize, $asmContigCount, $n50Size, $n50Count, $n50ContigSize, $n50ContigCount, $n50ScaffoldSize, $n50ScaffoldCount) = split('\t', $metaInfo{$asmId});
       # if asmSize is below the minimum, don't use it
        if ($asmSize < $minimalGenomeSize{$clade}) {
          printf STDERR "# %s underSized 0 %d %s %s < %s\n", $clade, ++$underSized{$clade}, $asmId, commify($asmSize), commify($minimalGenomeSize{$clade});
      printf STDERR "# ACK would be genArk assembly %s\n", $asmId if (defined($genArkAsm{$asmId}));
      printf STDERR "# ACK would be UCSC RR %s\n", $asmId if (defined($rrGcaGcfList{$asmId}));
 printf STDERR "# ACK metaInfo: %s '%s'\n", $asmId, $metaInfo{$asmId};
          next;
        }
      }
      $alreadyDone{$asmId} = 1;
      if (defined($genArkClade{$asmId})) {
           printf STDERR "# warning genArkClade{%s} does not = %s\n", $genArkClade{$asmId}, $clade if ($genArkClade{$asmId} ne $clade);
      }
      ++$checkedAsmIds;
      my $iucnSciName = "";
      if (defined($sciNames{$asmId})) {
        ++$ncbiSpeciesRecorded{$sciNames{$asmId}};
        if (! defined($genArkAsm{$asmId}) && !defined($rrGcaGcfList{$asmId})) {
          next if ($ncbiSpeciesRecorded{$sciNames{$asmId}} > $sciNameDisplayLimit);
          $iucnSciName = $sciNames{$asmId};
    $iucnSciName = $ncbiToIucnNames{$sciNames{$asmId}} if (defined($ncbiToIucnNames{$sciNames{$asmId}}));
          ++$iucnSpeciesRecorded{$iucnSciName};
        } else { 
          ++$genArkTooManySpecies if ($ncbiSpeciesRecorded{$sciNames{$asmId}} > $sciNameDisplayLimit);
        }
      } else {
        printf STDERR "# no sciName for: '%s' at %s\n", $asmId, commify($goodToGoCount + 1);
      }
      ++$cladeCount;
      if (! defined($cladeToGo{$clade})) {
        my @a;
        $cladeToGo{$clade} = \@a;
      }
      my $cPtr = $cladeToGo{$clade};
      push (@$cPtr, $asmId);
      ++$usedGenArk{$asmId} if (defined($genArkAsm{$asmId}));
      ++$countingUsedGenArk if (defined($genArkAsm{$asmId}));
      ++$acceptedAsmIds;
      ++$goodToGoCount;
      ++$ncbiSpeciesUsed if ( defined($sciNames{$asmId}) && defined($ncbiSpeciesRecorded{$sciNames{$asmId}}) && (1 == $ncbiSpeciesRecorded{$sciNames{$asmId}}) );
      ++$iucnSpeciesUsed if ( defined($iucnSpeciesRecorded{$iucnSciName}) && (1 == $iucnSpeciesRecorded{$iucnSciName}));
      ++$cladeCounts{$clade};
      my $assembliesAvailable = 0;
      if (defined($sciNames{$asmId})) {
        if (defined($sciNameCount{$sciNames{$asmId}})) {
          $assembliesAvailable = $sciNameCount{$sciNames{$asmId}};
        $maxDupAsm = $assembliesAvailable if ($assembliesAvailable > $maxDupAsm);
        }
        if ($assembliesAvailable > 1) {
           my $bPtr = $sciNameAsmList{$sciNames{$asmId}};
           foreach my $aId (@$bPtr) {
              next if (defined ($alreadyDone{$aId}));
              $alreadyDone{$aId} = 1;
              if ($aId ne $asmId) {
                if (defined($metaInfo{$aId})) {
                  my ($asmSize, $asmContigCount, $n50Size, $n50Count, $n50ContigSize, $n50ContigCount, $n50ScaffoldSize, $n50ScaffoldCount) = split('\t', $metaInfo{$aId});
                  # if asmSize is below the minimum, don't use it
                  if ($asmSize < $minimalGenomeSize{$clade}) {
                    if (! defined($genArkAsm{$aId}) && !defined($rrGcaGcfList{$aId}) ) {
                    printf STDERR "# %s underSized 1 %d %s %s < %s\n", $clade, ++$underSized{$clade}, $aId, commify($asmSize), commify($minimalGenomeSize{$clade});
      printf STDERR "# ACK would be genArk assembly %s\n", $aId if (defined($genArkAsm{$aId}));
      printf STDERR "# ACK would be UCSC RR %s\n", $aId if (defined($rrGcaGcfList{$aId}));
 printf STDERR "# ACK metaInfo: %s '%s'\n", $aId, $metaInfo{$aId};
                    next;
                    } else {
                      printf STDERR "# ACK %s genArk/RR too small at %s\n", $aId, commify($asmSize);
                    }
                  }
                }
                ++$ncbiSpeciesRecorded{$sciNames{$aId}};
                # the defined($sciName{$aId}) indicates it is a GenArk genome
                # always accept those even if it goes beyond the limit
                if ( ($ncbiSpeciesRecorded{$sciNames{$aId}} <= $sciNameDisplayLimit) || defined($genArkAsm{$aId}) || defined($rrGcaGcfList{$aId})) {
                  push (@$cPtr, $aId);
                  $usedGenArk{$aId} += 1 if (defined($genArkAsm{$aId}));
                  ++$countingUsedGenArk if (defined($genArkAsm{$asmId}));
                  ++$acceptedAsmIds;
                  ++$goodToGoCount;
                  ++$cladeCounts{$clade};
                }	#	under limit count or is GenArk assembly
              }	#	if ($aId ne $asmId)
           }	#	foreach my $aId (@$bPtr)
         }	#	if ($assembliesAvailable > 1)
      }	#	if (defined($sciNames{$asmId}))
   }	#	while (my $asmId = <FH>)
   close (FH);
   $totalGoodToGo += $goodToGoCount;
   printf STDERR "# %s\t%s\tgood to go %s, total good: %d\n", $clade, commify($cladeCount), $goodToGoCount, $totalGoodToGo;
   printf STDERR "# examined %d asmIds from\n#%s\n# %s\n# %s\n", $examinedAsmId, $refSeq, $genBank, $asmHubTsv;
   printf STDERR "# usedGenArk: %s total: %s\t%s\n", commify($countingUsedGenArk-$prevUsedGenArk), commify($countingUsedGenArk), $clade;
   $prevUsedGenArk = $countingUsedGenArk;
 }	#	foreach my $clade (@clades)
 
 printf STDERR "# would have knocked out %s GenArk assemblies over species count\n", commify($genArkTooManySpecies);
 printf STDERR "# checkedAsmIds: %d, acceptedAsmIds: %d, notInGoodToGo: %d\n", $checkedAsmIds, $acceptedAsmIds, $notInGoodToGo;
 
 printf STDERR "# total good to go %s, maxDupAsmCount: %s\n", commify($totalGoodToGo), commify($maxDupAsm);;
 
 printf STDERR "# should be GenArk: %s\n", commify($shouldBeGenArk);
 printf STDERR "# had originally %s assemblies from GenArk UCSC_GI.assemblyHubList.txt\n", commify($genArkCount);
 my $usedGenArk = 0;
 my $missedGenArk = 0;
 foreach my $genArkAsmId (sort keys %genArkAsm) {
   my $gClade = "n/a";
   $gClade = $genArkClade{$genArkAsmId} if (defined($genArkClade{$genArkAsmId}));
   if (defined($usedGenArk{$genArkAsmId})) {
     ++$usedGenArk;
     printf STDERR "# used genArk %s %s %s\n", $genArkAsmId, $gClade, $genArkAsm{$genArkAsmId} if ($usedGenArk < 5);
   } else {
     ++$missedGenArk;
     printf STDERR "# missed genArk %s %s %s\n", $genArkAsmId, $gClade, $genArkAsm{$genArkAsmId} if ($gClade !~ m/viral|bacteria/);
   }
 }
 printf STDERR "# should be UCSC RR %s, used GenArk: %s, missed GenArk: %s\n", commify($shouldBeUcsc), commify($usedGenArk), commify($missedGenArk);
 
 printf "<hr>\n";
 if ( 1 == 0 ) {
 printf "<button id='summaryCountsHideShow' onclick='gar.hideTable(\"summaryCounts\")'>[hide]</button>\n";
 printf "<table class='sortable borderOne' id='summaryCounts'>\n";
 printf "<caption style='text-align:center;'><b>===== summary counts =====</b></caption>\n";
 printf "<thead>\n";
 printf "<tr>\n";
 printf "<th>number of assemblies</th>\n";
 printf "<th>category of count</th>\n";
 printf "<th>table data in tsv<br>(tab separated value)<br>file format</th>\n";
 printf "<th>assembly minimal size<br>to filter out projects that<br>are not whole genomes</th>\n";
 printf "</tr>\n";
 printf "</thead><tbody>\n";
 printf "<tr><th style='text-align:right;'>%s</th><th>total number of NCBI assemblies under consideration</th><th>&nbsp;</th><th>&nbsp;</th></tr>\n", commify($ncbiTotalAssemblies);
 printf "<tr><th style='text-align:right;'>%s</th><th>number of unique species in NCBI assemblies</th><th>&nbsp;</th><th>&nbsp;</th></tr>\n", commify($ncbiUniqueSpecies);
 printf "<tr><th style='text-align:right;'>%s</th><th>number of unique NCBI species matched to IUCN classification</th><th>&nbsp;</th><th>&nbsp;</th></tr>\n", commify($ncbiSpeciesUsed);
 printf "<tr><th style='text-align:right;'>%s</th><th>number of IUCN species with CR/EN/VU classification</th><th>&nbsp;</th><th>&nbsp;</th></tr>\n", commify($iucnSpeciesCount);
 printf "<tr><th style='text-align:right;'>%s</th><th>number of such IUCN species matched to NCBI assemblies</th><th>&nbsp;</th><th>&nbsp;</th></tr>\n", commify($iucnSpeciesUsed);
 printf "<tr><th style='text-align:right;'>%s</th><th>total number of NCBI assemblies classified in these tables</th><th>&nbsp;</th><th>&nbsp;</th></tr>\n", commify($totalGoodToGo);
 foreach my $clade (@clades) {
   if (defined($cladeCounts{$clade})) {
     my $tsvFile = sprintf("%s.tableData.txt", $clade);
     printf "<tr><th style='text-align:right;'>%s</th>", commify($cladeCounts{$clade});
     printf "<th><a href='#%s'>%s</a></th>", $clade, $clade;
     printf "<th><a href='%s' target=_blank>%s</a></th>", $tsvFile, $tsvFile;
     printf "<th style='text-align:right;'>%s</th>", commify($minimalGenomeSize{$clade});
     printf "</tr>\n";
   }
 }
 print "</tbody></table>\n";
 printf "<hr>\n";
 
 sub sectionDiv($) {
   my ($clade) = @_;
   printf "<a id='%sSection'></a>\n", $clade;
   printf "<table class='sectionDiv'><tr>\n";
   printf "<td><button class='hideShowButton' id='%sHideShow' onclick='gar.hideTable(\"%s\")'>[hide]</button><b>&nbsp;%s</b></td>\n", $clade, $clade, $clade;
   foreach my $c (@clades) {
     if ($c ne $clade) {
       printf "<td><a href=#%sSection>%s</a></td>\n", $c, $c;
     } else {
       printf "<td><em>page sections</em></td>\n";
     }
   }
   printf "<td><a href='#pageTop'>top of page</a></td>\n";
   printf "</table>\n";
 }
 }	#	if ( 1 == 0 )
 
 # count all assemblies in all clades
 my $totalAssemblies = 0;
 foreach my $c (@clades) {
   $totalAssemblies += $cladeCounts{$c};
 }
 
 printf "<!-- to get the pull-down menu items centered together -->\n";
 printf "<div style='text-align: center;'><!-- this will cause the next div to center -->\n";
 printf "  <div style='display: inline-block'>\n";
 
 printf "<div class='pullDownMenu'>\n";
 printf "  <span id='speciesSelectAnchor'>choose clades to view/hide &#9660;</span>\n";
 printf "  <div class='pullDownMenuContent'>\n";
 printf "  <ul id='checkBoxSpeciesSelect'>\n";
 printf "    <li><label><input class='showAll' type='checkbox' onchange='gar.visCheckBox(this)' id='allCheckBox0' value='all' checked><span class='showAllLabel'> show all</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='primatesCheckBox' value='primates' checked><span id='primatesLabel'> primates</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='mammalsCheckBox' value='mammals' checked><span id='mammalsLabel'> mammals</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='birdsCheckBox' value='birds' checked><span id='birdsLabel'> birds</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='fishCheckBox' value='fish' checked><span id='fishLabel'> fish</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='vertebrateCheckBox' value='vertebrate' checked><span id='vertebrateLabel'> vertebrate</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='invertebratesCheckBox' value='invertebrates' checked><span id='invertebratesLabel'> invertebrates</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='plantsCheckBox' value='plants' checked><span id='plantsLabel'> plants</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='fungiCheckBox' value='fungi' checked><span id='fungiLabel'> fungi</span></label></li>\n";
 printf "  </ul>\n";
 printf "  </div>\n";
 printf "</div>\n";
 
 printf "<div style='width: 260px;' class='pullDownMenu'>\n";
 printf "  <span style='text-align: center;' id='assemblyTypeAnchor'>select assembly type to display &#9660;</span>\n";
 printf "  <div class='pullDownMenuContent'>\n";
 printf "  <ul id='checkBoxAssemblyType'>\n";
 printf "    <li><label><input class='showAll' type='checkbox' onchange='gar.visCheckBox(this)' id='allCheckBox1' value='all' checked><span class='showAllLabel'> show all</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='gakCheckBox' value='gak' checked><span id='gakLabel'> Existing browser</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='garCheckBox' value='gar' checked><span id='garLabel'> Request browser</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='gcaCheckBox' value='gca' checked><span id='gcaLabel'> GCA/GenBank</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='gcfCheckBox' value='gcf' checked><span id='gcfLabel'> GCF/RefSeq</span></label></li>\n";
 printf "    <li><label><input class='hideShow' type='checkbox' onchange='gar.visCheckBox(this)' id='iucnCheckBox' value='hasIucn' checked><span id='iucnLabel'> IUCN</span></label></li>\n";
 printf "   </ul>\n";
 printf "  </div>\n";
 printf "</div>\n";
 
 printf "<div style='width: 240px;' class='pullDownMenu'>\n";
 printf "  <span id='columnSelectAnchor'>show/hide columns &#9660;</span>\n";
 printf "  <div class='pullDownMenuContent'>\n";
 printf "  <ul id='checkBoxColumnSelect'>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='comNameCheckBox' value='comName' checked> English common name</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='sciNameCheckBox' value='sciName' checked> scientific name</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='asmIdCheckBox' value='asmId' checked> NCBI Assembly</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='asmSizeCheckBox' value='asmSize'> assembly size</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='seqCountCheckBox' value='seqCount'> sequence count</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='scafN50CheckBox' value='scafN50'> scaffold N50 length (L50)</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='ctgN50CheckBox' value='ctgN50'> contig N50 length (L50)</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='IUCNCheckBox' value='IUCN'> IUCN status</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='taxIdCheckBox' value='taxId'> NCBI taxonomy ID</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='asmDateCheckBox' value='asmDate'> assembly date</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='bioSampleCheckBox' value='bioSample'> BioSample</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='bioProjectCheckBox' value='bioProject'> BioProject</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='submitterCheckBox' value='submitter'> assembly submitter</label></li>\n";
 printf "    <li><label><input class='columnCheckBox' type='checkbox' onchange='gar.resetColumnVis(this)' id='cladeCheckBox' value='clade'> clade</label></li>\n";
 printf "  </ul>\n";
 printf "  </div>\n";
 printf "</div>\n\n";
 printf "  </div>        <!-- display inline-block to be 'text' centered -->\n";
 printf "</div>  <!-- this parent div is text-align: center to center children -->\n\n";
 
 printf "<table style='width: 100%%;' class='borderOne' id='loadingStripes'>\n";
 printf "<caption><h2>. . . please wait while page loads . . .</h2></caption>\n";
 printf "</table>\n\n";
 
 printf "<div style='text-align: center;'><!-- this will cause the next div to center -->\n";
 printf "  <div style='display: inline-block'>\n\n";
 
 printf "<h2 style='display: none;' id='counterDisplay'>%s total assemblies : use the selection menus to select subsets</h2>\n\n", commify($totalAssemblies);
 
 ##############################################################################
 ##  begin single table output, start the table and the header
 ##
 ## table starts out as display: none and will be reset to 'table' after
 ## page load.  Saves a lot of time for Chrome browsers, however the page
 ## is still not usable until much time later.
 ##############################################################################
 printf "<table style='display: none;' class='sortable borderOne cladeTable' id='dataTable'>\n";
 
 printf "<colgroup id='colDefinitions'>\n";
 printf "<col id='viewReq' span='1' class=colGViewReq>\n";
 printf "<col id='comName' span='1' class=colGComName>\n";
 printf "<col id='sciName' span='1' class=colGSciName>\n";
 printf "<col id='asmId' span='1' class=colGAsmId>\n";
 printf "<col id='asmSize' span='1' class=colGAsmSize>\n";
 printf "<col id='seqCount' span='1' class=colGAsmSeqCount>\n";
 printf "<col id='scafN50' span='1' class=colGScafN50>\n";
 printf "<col id='ctgN50' span='1' class=colGContigN50>\n";
 printf "<col id='IUCN' span='1' class=colGIUCN>\n";
 printf "<col id='taxId' span='1' class=colGTaxId>\n";
 printf "<col id='asmDate' span='1' class=colGAsmDate>\n";
 printf "<col id='bioSample' span='1' class=colGBioSample>\n";
 printf "<col id='bioProject' span='1' class=colGBioProject>\n";
 printf "<col id='submitter' span='1' class=colGSubmitter>\n";
 printf "<col id='clade' span='1' class=colGClade>\n";
 printf "</colgroup>\n";
 
 printf "<thead>\n";
 printf "<tr>\n";
 printf "  <th class='colViewReq'><div class='tooltip'>view/request &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'><em>'view'</em> opens the genome browser for an existing assembly, <em>'request'</em> opens an assembly request form.</span></div></th>\n";
 printf "  <th class='colComName'><div class='tooltip'>English common name &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>English common name</span></div></th>\n";
 printf "  <th class='colSciName'><div class='tooltip'>scientific name (count) &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>Links to Google image search. Count shows the number of assemblies available for this organism.</span></div></th>\n";
 printf "  <th class='colAsmId'><div class='tooltip'>NCBI Assembly &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>Links to NCBI resource record.</span></div></th>\n";
 printf "  <th class='colAsmSize'><div class='tooltip'>assembly<br>size &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>Number of nucleotides in the assembly.</span></div></th>\n";
 printf "  <th class='colAsmSeqCount'><div class='tooltip'>sequence<br>count &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>The number of sequences in this assembly.</span></div></th>\n";
 printf "  <th class='colScafN50'><div class='tooltip'>scaffold N50<br>length (L50) &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'><a href='https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics' target=_blank>N50 (L50)</a> length.</span></div> </th>\n";
 printf "  <th class='colContigN50'><div class='tooltip'>contig N50<br>length (L50) &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'><a href='https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics' target=_blank>N50 (L50)</a> length.</span></div></th>\n";
 printf "  <th class='colIUCN'><div class='tooltip'>IUCN &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>Links to <a href='https://www.iucnredlist.org/' target=_blank>IUCN Red List</a> of Threatened Species (version 2021-3) <span style='color:%s;'>CR - Critical</span> / <span style='color:%s;'>EN - Endangered</span> / <span style='color:%s;'>VU - Vulnerable</span></span></div></th>\n", $statusColors{"CR"}, $statusColors{"EN"}, $statusColors{"VU"};
 printf "  <th class='colTaxId'><div class='tooltip'>NCBI taxID &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>Links to <a href='https://www.ncbi.nlm.nih.gov/taxonomy' target='_blank'>NCBI Taxonomy</a> database.</span></div></th>\n";
 printf "  <th class='colAsmDate'><div class='tooltip'>assembly<br>date &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>Date submitted to <a href='https://www.ncbi.nlm.nih.gov/assembly' target=_blank>NCBI Assembly</a> database.</span></div></th>\n";
 printf "  <th class='colBioSample sorttable_alpha'><div class='tooltip'>BioSample &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>BioSample ID at <a href='https://www.ncbi.nlm.nih.gov/biosample' target=_blank>NCBI</a>.</span></div></th>\n";
 printf "  <th class='colBioProject sorttable_alpha'><div class='tooltip'>BioProject &#9432;<span onclick='event.stopPropagation()' class='tooltiptext'>BioProject ID at <a href='https://www.ncbi.nlm.nih.gov/bioproject' target=_blank>NCBI</a>.</span></div></th>\n";
 printf "  <th class='colSubmitter sorttable_alpha'><div class='tooltip'>Assembly submitter &#9432;<span onclick='event.stopPropagation()' class='tooltiptextright'>Person or group who submitted to <a href='https://www.ncbi.nlm.nih.gov/assembly' target=_blank>NCBI Assembly</a> database.</span></div></th>\n";
 printf "  <th class='colClade'><div class='tooltip'>clade &#9432;<span onclick='event.stopPropagation()' class='tooltiptextright'>Clade of this organism.</span></div></th>\n";
 printf "</tr>\n";
 printf "</thead><tbody>\n";
 
 my %equivalentNamesUsed;	# key is NCBI sciName, value is IUCN sciName
 my $pageSectionCount = 0;
 
 my %checkDupAsmId;	# key is asmId, value is count of times seen
 
 my %cladeSciNameCounts;	# key is clade, value is number of different
 			# scientific names
 
 my %gcfGcaCounts;	# key is GCF or GCA, value is count of each
 my $asmCountInTable = 0;	# counting the rows output
 my %statusCounts;	# key is status: CR EN VU, value is count
 my $totalAssemblySize = 0;	# sum of all assembly sizes
 
 my $outputGenArkRR = 0;
 my %outputGenArk;	# key is asmId, value is clade
 my %outputRR;	# key is asmId, value is clade
 
 foreach my $clade (@clades) {
   my $cPtr = $cladeToGo{$clade};
   my $countThisClade = scalar(@$cPtr);
   printf STDERR "# working on clade '%s', count: %s\n", $clade, commify($countThisClade);
 
 ##  sectionDiv($clade);	# starting new clade table
 
   ++$pageSectionCount;
   my $totalContigCounts = 0;
   my $underSized = 0;
   my $noCommonName = 0;
   my $suppressedCount = 0;
 
   ######################## rows of per clade table output here ################
   my $tsvFile = sprintf("%s.tableData.txt", $clade);
   open (PC, ">$tsvFile") or die "can not write to $tsvFile";
 
   foreach my $asmId (@$cPtr) {
      if (defined($checkDupAsmId{$asmId})) {
       printf STDERR "# what: duplicate asmId: %s in clade %s\n", $asmId, $clade;
         $checkDupAsmId{$asmId} += 1;
      } else {
         $checkDupAsmId{$asmId} = 1;
      }
     my $assembliesAvailable = 0;
     if (defined($sciNames{$asmId})) {
       if (defined($sciNameCount{$sciNames{$asmId}})) {
         $assembliesAvailable = $sciNameCount{$sciNames{$asmId}};
       }
     }
     if (defined ($asmSuppressed{$asmId})) {
       if (!defined($rrGcaGcfList{$asmId})) {
         if (! defined($genArkAsm{$asmId}) && !defined($rrGcaGcfList{$asmId})) {
         ++$suppressedCount;
         printf STDERR "# suppressed $asmId\n" if ($suppressedCount < 5);
         next;
         } else {
           printf STDERR "# genArk/RR %s would have been suppressed\n", $asmId;
         }
       }
     }
     my $commonName = "n/a";
     if (defined($ncbiCommonName{$asmId})) {
       $commonName = $ncbiCommonName{$asmId};
       if ("n/a" eq $commonName) {
         printf STDERR "# getting n/a commonName from ncbiCommonName{%s}\n", $asmId;
       }
     } elsif (defined($comName{$asmId})) {
       $commonName = $comName{$asmId};
       if ("n/a" eq $commonName) {
         printf STDERR "# getting n/a commonName from comName{%s}\n", $asmId;
       }
     } else {
       if (defined($genArkAsm{$asmId}) || defined($rrGcaGcfList{$asmId})) {
         printf STDERR "# ACK missed genArk/RR due to no common name for %s\n", $asmId;
       }
       ++$noCommonName;
       printf STDERR "# no commonName for %s in ncbiCommonName or comName\n", $asmId if ($noCommonName < 5);
       next;
     }
 
 #   if (! defined($gcxCountry{$asmId})) {
 #      printf STDERR "# no country for $asmId, date: %s, submitter: %s\n", $gcxDate{$asmId}, $gcxSubmitter{$asmId};
 #      next;
 #    }
 #    if ("n/a" eq $gcxCountry{$asmId}) {
 #      printf STDERR "# country is n/a $asmId\n";
 #      next;
 #    }
   my ($p0, $p1, $p2) = split('_', $asmId, 3);
   my $accessionId = "${p0}_${p1}";
   my $gcX = substr($asmId, 0, 3);
   my $d0 = substr($asmId, 4, 3);
   my $d1 = substr($asmId, 7, 3);
   my $d2 = substr($asmId, 10, 3);
   my $buildDir = "/hive/data/outside/ncbi/genomes/$gcX/$d0/$d1/$d2/$asmId";
   my $asmRpt = "$buildDir/${asmId}_assembly_report.txt";
   my $asmFna = "$buildDir/${asmId}_genomic.fna.gz";
   my $browserUrl = sprintf("/h/%s", $accessionId);
   my $arkDownload = sprintf("https://hgdownload.soe.ucsc.edu/hubs/%s/%s/%s/%s/%s/", $gcX, $d0, $d1, $d2, $accessionId);
   my $destDir = "/hive/data/outside/ncbi/genomes/sizes/$gcX/$d0/$d1/$d2";
   my $chromInfo = "/hive/data/outside/ncbi/genomes/sizes/$gcX/$d0/$d1/$d2/${asmId}.chromInfo.txt";
   my $n50Txt = "/hive/data/outside/ncbi/genomes/sizes/$gcX/$d0/$d1/$d2/${asmId}.n50.txt";
   my $contigN50 = "/hive/data/outside/ncbi/genomes/sizes/$gcX/$d0/$d1/$d2/${asmId}.contigs.n50.txt";
   my $scaffoldN50 = "/hive/data/outside/ncbi/genomes/sizes/$gcX/$d0/$d1/$d2/${asmId}.scaffolds.n50.txt";
   my $asmSize = 0;
   my $asmContigCount = 0;
   my $n50Size = 0;
   my $n50Count = 0;
   my $n50ContigSize = 0;
   my $n50ContigCount = 0;
   my $n50ScaffoldSize = 0;
   my $n50ScaffoldCount = 0;
   my $bioSample = "";
   my $bioProject = "";
   if (defined($asmReportData{$asmId})) {
      (undef, undef, $bioSample, $bioProject, undef) = split('\t', $asmReportData{$asmId}, 5);
   }
   if (defined($metaInfo{$asmId})) {
    ($asmSize, $asmContigCount, $n50Size, $n50Count, $n50ContigSize, $n50ContigCount, $n50ScaffoldSize, $n50ScaffoldCount) = split('\t', $metaInfo{$asmId});
   } else {
   my ($dev, $ino, $mode, $nlink, $uid, $gid, $rdev, $size, $atime, $mtime, $ctime, $blksize, $blocks);
   my $fnaModTime = 0;
   if (-s "$asmFna") {
     ($dev, $ino, $mode, $nlink, $uid, $gid, $rdev, $size, $atime, $mtime, $ctime, $blksize, $blocks) = stat($asmFna);
     $fnaModTime = $mtime;
   }
   my $ciModTime = 0;
   if ( -s "$chromInfo" ) {
     ($dev, $ino, $mode, $nlink, $uid, $gid, $rdev, $size, $atime, $mtime, $ctime, $blksize, $blocks) = stat($chromInfo);
     $ciModTime = $mtime;
   }
   if ($fnaModTime > $ciModTime) {
     printf STDERR "# new %s\n", $chromInfo;
     printf STDERR "# from %s\n", $asmFna;
     print `mkdir -p $destDir`;
     print `faSize -detailed $asmFna | sort -k2,2nr > $chromInfo`;
     print `touch -r $asmFna $chromInfo`;
   }
   if ( -s "$chromInfo" ) {
     ($asmSize, $asmContigCount) = sizeUpChromInfo($chromInfo);
     if ( ! -s "$n50Txt" ) {
       print `n50.pl "$chromInfo" > "$n50Txt" 2>&1`;
     }
     ($n50Size, $n50Count) = readN50($n50Txt);
     if ( -s "$contigN50" ) {
       ($n50ContigSize, $n50ContigCount) = readN50($contigN50);
     }
     if ( -s "$scaffoldN50" ) {
       ($n50ScaffoldSize, $n50ScaffoldCount) = readN50($scaffoldN50);
     }
   } else {
     printf STDERR "# chromInfo missing: %s\n", $asmId;
     printf STDERR "# %s\n", $chromInfo;
   }
    die "ERROR duplicate newMetaInfo{$asmId}" if (defined($newMetaInfo{$asmId}));
    die "ERROR duplicate metaInfo{$asmId} for newMetaInfo{$asmId}" if (defined($metaInfo{$asmId}));
    $newMetaInfo{$asmId} = join("\t", ($asmSize, $asmContigCount, $n50Size, $n50Count, $n50ContigSize, $n50ContigCount, $n50ScaffoldSize, $n50ScaffoldCount) );
   }	# else if (defined($metaInfo{$asmId}))
   # if asmSize is below the minimum, don't use it
   if ($asmSize < $minimalGenomeSize{$clade}) {
     printf STDERR "# %s underSized 2 %d %s %s < %s\n", $clade, ++$underSized, $asmId, commify($asmSize), commify($minimalGenomeSize{$clade});
      printf STDERR "# ACK would be genArk assembly %s\n", $asmId if (defined($genArkAsm{$asmId}));
      printf STDERR "# ACK would be UCSC RR %s\n", $asmId if (defined($rrGcaGcfList{$asmId}));
      next;
   }
   my $iucnStatus = "&nbsp;";
   my $iucnLink = "";
   if (defined($sciNames{$asmId})) {
      my $iucnSciName = $sciNames{$asmId};
  $iucnSciName = $ncbiToIucnNames{$sciNames{$asmId}} if (defined($ncbiToIucnNames{$sciNames{$asmId}}));
      $iucnLink = "https://www.iucnredlist.org/species/$iucnLink{$iucnSciName}" if (defined($iucnLink{$iucnSciName}));
      if ($iucnSciName ne $sciNames{$asmId}) {
        $equivalentNamesUsed{$sciNames{$asmId}} = $iucnSciName;
      }
      if (defined($iucnSciNames{$iucnSciName})) {
        $iucnStatus = $iucnSciNames{$iucnSciName};
      }
   }
   ++$asmCountInTable;
   my $statusColor = "";
   if ($iucnStatus ne "&nbsp;") {
     $statusColor = $statusColors{$iucnStatus};
     ++$statusCounts{$iucnStatus};
   }
 
   ############# starting a table row  #################################
   ++$outputGenArkRR if (defined($rrGcaGcfList{$asmId}) || defined($genArkAsm{$asmId}));
   $outputGenArk{$asmId} = $clade if (defined($genArkAsm{$asmId}));
   $outputRR{$asmId} = $clade if (defined($rrGcaGcfList{$asmId}));
   if ($asmId =~ m/^GCF/) {
     $gcfGcaCounts{'GCF'} += 1;
   } elsif ($asmId =~ m/GCA/) {
     $gcfGcaCounts{'GCA'} += 1;
   }
   ### If equivalent to UCSC database browser, make reference to RR browser
   my $ucscDb = "";
   $ucscDb = "/" . $rrGcaGcfList{$asmId} if (defined($rrGcaGcfList{$asmId}));
   if (length($ucscDb)) {
      $browserUrl = sprintf("/cgi-bin/hgTracks?db=%s", $rrGcaGcfList{$asmId});
   }
 
-  printf PC "%d", $asmCountInTable;	# start a line output to clade.tableData.tsv
+  printf PC "%s", $browserUrl;	# start a line output to clade.tableData.tsv
 
   ## count number of different scientific names used in this clade table
   if (!defined($cladeSciNameCounts{$clade})) {
     my %h;
     $cladeSciNameCounts{$clade} = \%h;
   }
   my $csnPtr = $cladeSciNameCounts{$clade};
   $csnPtr->{$sciNames{$asmId}} += 1 if (defined($sciNames{$asmId}));
   my $rowClass = "";
   my $gcaGcfClass = "gca";
   $gcaGcfClass = "gcf" if ($asmId =~ m/^GCF/);
   $gcaGcfClass .= " hasIucn" if (length($iucnLink));
   if (defined($comName{$asmId})) {
     if (defined($rrGcaGcfList{$asmId})) {
       $rowClass = " class='ucscDb $gcaGcfClass $clade'"; # present in UCSC db
     } else {
       $rowClass = " class='gak $gcaGcfClass $clade'"; # present in GenArk
     }
   } else { # can be requested
     if (defined($rrGcaGcfList{$asmId})) {
       $rowClass = " class='ucscDb $gcaGcfClass $clade'"; # present in UCSC db
     } else {
       $rowClass = " class='gar $gcaGcfClass $clade'"; # available for request
     }
   }
 ### can override CSS settings here
 ###    $rowClass = " class='gar' style='display: none;'";
 
   # experiment with hiding all rows over 500 count to see if that helps
   # chrom browser initial loading performance
   # try out the table with out any count, just get the row started
   if (length($statusColor)) {
      my $statusClass = sprintf(" style='color:%s;", $statusColor);
      # let's see what nostatus looks like
      $statusClass = "";
      if ($asmCountInTable > 500) {
        printf "<tr%s%s style='display:none;'>", $rowClass, $statusClass;
      } else {
        printf "<tr%s%s>", $rowClass, $statusClass;
      }
   } else {
      if ($asmCountInTable > 500) {
        printf "<tr%s style='display:none;'>", $rowClass;
      } else {
        printf "<tr%s>", $rowClass;
      }
   }
   ############# trying out a first column that is just the button or link
 
   ############# first column, common name link to browser or request button ##
   if (defined($comName{$asmId})) {
      printf "<th style='text-align:center;'><a href='%s' target=_blank>view</a></th>", $browserUrl;
      printf PC "\tview";	# output to clade.tableData.tsv
      printf "<th style='text-align:left;'>%s</th>", $commonName;
   } else {
      if (length($ucscDb)) {
        printf "<th style='text-align:center;'><a href='%s' target=_blank>view</a></th>", $browserUrl;
        printf PC "\tview";	# output to clade.tableData.tsv
        printf "<th style='text-align:left;'>%s</th>", $commonName;
      } else {
        printf "<th style='text-align:center;'><button type='button' onclick='gar.openModal(this)' name='%s'>request</button></th>", $asmId;
        printf PC "\trequest";	# output to clade.tableData.tsv
        printf "<th style='text-align:left;'>%s</th>", $commonName;
      }
   }
   printf PC "\t%s", $commonName;	# output to clade.tableData.tsv
 
   ############# second column, scientific name and google image search #########
   if (defined($sciNames{$asmId})) {
     my $noSpace = $sciNames{$asmId};
     $noSpace =~ s/ /+/g;
     my $imgSearchUrl="https://images.google.com/images?q=$noSpace&um=1&hl=en&safe=active&nfpr=1&tbs=il:cl";
     if ($assembliesAvailable > 1) {
       printf "<td><a href='%s' target=_blank>%s</a>&nbsp;(%s)</td>", $imgSearchUrl, $sciNames{$asmId}, commify($assembliesAvailable);
     } else {
       printf "<td><a href='%s' target=_blank>%s</a></td>", $imgSearchUrl, $sciNames{$asmId};
     }
     printf PC "\t%s", $sciNames{$asmId};	# output to clade.tableData.txt
   } else {
     printf "<td>n/a</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# third column,  NCBI assembly and link to NCBI ############
   my $asmUrl = "https://www.ncbi.nlm.nih.gov/assembly/$accessionId";
   printf "<td><a href='%s' target=_blank>%s%s</a></td>", $asmUrl, $asmId, $ucscDb;
   printf PC "\t%s", $asmId;	# output to clade.tableData.txt
 
   ############# fourth column,  assembly size ################
   if ($asmSize > 0) {
     $totalAssemblySize += $asmSize;
     printf "<td style='display:none; text-align:right;'>%s</td>", commify($asmSize);
     printf PC "\t%d", $asmSize;	# output to clade.tableData.txt
   } else {
     printf "<td style='display:none;'>&nbsp;</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# fifth column,  sequence count ################
   if ($asmContigCount > 0) {
     $totalContigCounts += $asmContigCount;
     printf "<td style='display:none; text-align:right;'>%s</td>", commify($asmContigCount);
     printf PC "\t%d", $asmContigCount;	# output to clade.tableData.txt
   } else {
     printf "<td style='display:none;'>&nbsp;</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# sixth, seventh columns, N50 for scaffold, contig ##############
   if ($n50ScaffoldSize > 0 ) {
     n50Cell($n50ScaffoldSize, $n50ScaffoldCount, \*PC);
   } else {	# substitute assembly N50 when no scaffold N50 available
     n50Cell($n50Size, $n50Count, \*PC);
   }
   n50Cell($n50ContigSize, $n50ContigCount, \*PC);
 
   ############# eighth column,  IUCN status and link ################
   if (length($iucnLink) > 0) {
     printf "<td class='iucn%s' style='display:none;'><a href='%s' target=_blank>%s</a></td>", $iucnStatus, $iucnLink, $iucnStatus;
   } else {
     printf "<td class='iucnNone' style='display:none;'>%s</td>", $iucnStatus;
   }
   printf PC "\t%s", $iucnStatus;	# output to clade.tableData.txt
 
   ############# ninth column,  taxId and link to NCBI ################
   if (defined($asmTaxId{$asmId})) {
     my $taxUrl = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$asmTaxId{$asmId}";
     printf "<td style='display:none; text-align:right;'><a href='%s' target=_blank>%s</a></td>", $taxUrl, $asmTaxId{$asmId};
     printf PC "\t%s", $asmTaxId{$asmId};	# output to clade.tableData.txt
   } else {
     printf "<td style='display:none;'>n/a</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# tenth column,  assembly date ################
   if (defined($asmDate{$asmId})) {
     printf "<td style='display:none;'>%s</td>", $asmDate{$asmId};
     printf PC "\t%s", $asmDate{$asmId};	# output to clade.tableData.txt
   } else {
     printf "<td style='display:none;'>n/a</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# eleventh column,  bioSample ################
   if (length($bioSample) && $bioSample !~ m#n/a#) {
     printf "<td style='display:none; text-align:left;'><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>", $bioSample, $bioSample;
     printf PC "\t%s", $bioSample;	# output to clade.tableData.txt
   } else {
     printf "<td style='display:none; text-align:left;'>&nbsp;</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# twelveth column,  bioProject ################
   if (length($bioProject) && $bioProject !~ m#n/a#) {
     printf "<td style='display:none; text-align:left;'><a href='https://www.ncbi.nlm.nih.gov/bioproject/?term=%s' target=_blank>%s</a></td>", $bioProject, $bioProject;
     printf PC "\t%s", $bioProject;	# output to clade.tableData.txt
 
   } else {
     printf "<td style='display:none; text-align:left;'>&nbsp;</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# eleventh column,  submitter ################
   $asmUrl = "https://www.ncbi.nlm.nih.gov/assembly/$accessionId";
   if (defined($asmSubmitter{$asmId})) {
     my $submitterSortKey = lc($asmSubmitter{$asmId});
     $submitterSortKey =~ s/ //g;
     $submitterSortKey =~ s/[^a-z0-9]//ig;
     printf "<td sorttable_customkey='%s' style='display:none;'>%s</td>", substr($submitterSortKey,0,20), $asmSubmitter{$asmId};
     printf PC "\t%s", $asmSubmitter{$asmId};	# output to clade.tableData.txt
   } else {
     printf "<td sorttable_customkey='n/a' style='display:none;'>n/a</td>";
     printf PC "\t%s", "n/a";	# output to clade.tableData.txt
   }
 
   ############# twelveth column,  clade ################
   printf "<td style='display:none;'>%s</td>\n", $clade;
   printf PC "\t%s", $clade;
 
   printf PC "\n";	# finished a line output to clade.tableData.txt
   printf "</tr>\n";
   }	#	foreach my $asmId (@$cPtr)
   close (PC);	# finished with clade.tableData.txt output
   printf STDERR "# no commonName %s for clade %s\n", commify($noCommonName), $clade;
   printf STDERR "# suppressed %s for clade %s\n", commify($suppressedCount), $clade;
 }	#	foreach my $clade (@clades)
 
 printf STDERR "# output %s genArk or RR assemblies\n", commify($outputGenArkRR);
 
 ##########################################################################
 ## single table is finished, output the end of tbody and the tfoot row
 ##########################################################################
 if ($asmCountInTable > 1) {
   my $crCount = 0;
   my $enCount = 0;
   my $vuCount = 0;
   foreach my $statId (keys %statusCounts) {
     $crCount = $statusCounts{$statId} if ($statId eq "CR");
     $enCount = $statusCounts{$statId} if ($statId eq "EN");
     $vuCount = $statusCounts{$statId} if ($statId eq "VU");
   }
   my $sciNameTotal = 0;
   foreach my $c (@clades) {
     my $csnPtr = $cladeSciNameCounts{$c};
     my $sciNameTotal = 0;
     foreach my $cladeSciName (keys %$csnPtr) {
       ++$sciNameTotal;
     }
   }
   printf "
 </tbody>
 <!--
 <tfoot><tr><th>assemblies:&nbsp;%s</th>
   <th>Species:&nbsp;%s</th>
   <td>GenBank: %s RefSeq %s</td>
   <td>%s nucleotides</td>
   <td colspan=4><span style='color:%s;'>CR&nbsp;%s</span><span style='color:%s;'>&nbsp;EN&nbsp;%s</span><span style='color:%s;'>&nbsp;VU&nbsp;%s</span></td>
   <td>submittors</td>
 </tr>
 ", commify($asmCountInTable), commify($sciNameTotal), commify($gcfGcaCounts{'GCA'}), commify($gcfGcaCounts{'GCF'}), commify($totalAssemblySize), $criticalColor, commify($crCount), $endangeredColor, commify($enCount), $vulnerableColor, commify($vuCount);
   printf "</tfoot>
 -->
 </table>\n";
 } else {
   print "</tbody></table>\n";
 }
 
 printf "  </div>        <!-- display inline-block to be 'text' centered -->\n";
 printf "</div>  <!-- this parent div is text-align: center to center children -->\n\n";
 
 ############################################################################
 
 if ( 1 == 0) {
 printf "<hr>\n";
 printf "<a id='nameTranslateSection'></a>\n";
 printf "<p><a href='#pageTop'>=== back to top of page ===</a></p>\n";
 printf "<p>
 Please note, in some cases the IUCN scientific name was translated to the
 scientific name used in the NCBI assembly to establish an equivalence
 between the two data sources.  Please beware of this translation when
 interpreting the IUCN status.
 </p>\n";
 printf "<button id='nameTranslationHideShow' onclick='gar.hideTable(\"nameTranslation\")'>[hide]</button>\n";
 printf "<table class='sortable borderOne' id='nameTranslation'>\n";
 printf "<caption style='text-align:center;'><b>IUCN to NCBI scientific name translation</b></caption>\n";
 printf "<thead>\n";
 printf "<tr>\n";
 printf "<th>NCBI assembly scientific name</th>\n";
 printf "<th>translated to IUCN scientific name</th>\n";
 printf "</thead><tbody>\n";
 foreach my $ncbiName (sort keys(%equivalentNamesUsed)) {
    printf "<tr><th>%s</th><th>%s</th></tr>\n", $ncbiName, $equivalentNamesUsed{$ncbiName};
 }
 print "</tbody></table>\n";
 }	#	if ( 1 == 0)
 
 ######### output new metaInfo to accumulating metaInfo file
 my $newMetaInfoCount = 0;
 foreach my $asmId (sort keys %newMetaInfo) {
   ++$newMetaInfoCount;
 }
 if ($newMetaInfoCount > 0) {
 printf STDERR "# adding %d new items to ../accumulateMetaInfo.tsv\n", $newMetaInfoCount;
 if (-s "../accumulateMetaInfo.tsv" ) {
   open (FH, ">>../accumulateMetaInfo.tsv") or die "can not append to ../accumulateMetaInfo.tsv";
 } else {
   open (FH, ">../accumulateMetaInfo.tsv") or die "can not write to ../accumulateMetaInfo.tsv";
 }
 foreach my $asmId (sort keys %newMetaInfo) {
   printf FH "%s\t%s\n", $asmId, $newMetaInfo{$asmId};
   printf STDERR "# new metaData for %s\n", $asmId;
   ++$newMetaInfoCount;
 }
 close (FH);
 } else {
   printf STDERR "# no new metaInfo\n";
 }
 
 my $beenThere = 0;
 printf STDERR "# checking missing genArk assemblies in output\n";
 foreach my $gAsmId (sort keys %genArkAsm) {
   ++$beenThere if ($genArkClade{$gAsmId} !~ m/viral|bacteria/);
   if (!defined($outputGenArk{$gAsmId})) {
     printf STDERR "# not output genArk %s\t%s\n", $gAsmId, $genArkClade{$gAsmId}
  if ($genArkClade{$gAsmId} !~ m/viral|bacteria/);
   }
 }
 printf STDERR "# there were %s GenArk potential to output\n", commify($beenThere);
 
 $beenThere = 0;
 
 printf STDERR "# checking missing RR assemblies in output\n";
 
 foreach my $rrAsmId (sort keys %rrGcaGcfList) {
   ++$beenThere;
   if (!defined($outputRR{$rrAsmId})) {
    printf STDERR "# not output RR %s\t%s\n", $rrAsmId, $rrGcaGcfList{$rrAsmId};
   }
 }
 printf STDERR "# there were %s RR potential to output\n", commify($beenThere);
 
 printf STDERR "# done at exit\n";
 exit 0;
 
 __END__
 
 my $count = 0;
 foreach my $asmId (sort keys %gcxCountry) {
   next if (defined ($asmSuppressed{$asmId}));
   next if (! defined($gcxCountry{$asmId}));
   next if (! defined($sciName{$asmId}));
   next if ("n/a" eq $gcxCountry{$asmId});
 ##########################################################################
 # found discussion of google image search URL at:
 # https://stackoverflow.com/questions/21530274/format-for-a-url-that-goes-to-google-image-search
 # did not work:
 #    my $imgSearchUrl="https://www.google.com/search?q=$noSpace&tbm=isch";
 # um=1&hl=en&safe=active&nfpr=1
 # and
 # http://devcoma.blogspot.com/2017/04/google-search-parameters-resources.html
 # as_rights=cc_publicdomain
 #     my $imgSearchUrl="https://images.google.com/images?q=$noSpace&um=1&hl=en&safe=active&nfpr=1";
 # safe=active == safe search on
 # tbs=il:cl - limit result to creative commons license
 }