src/hg/makeDb/doc/asmHubs/mkAsmStats.pl a3221ce060e8efe2e9ef46392625606896f64f96

a3221ce060e8efe2e9ef46392625606896f64f96
hiram
  Fri May 8 23:06:59 2020 -0700
do not print links to other assembly hubs from VGP index pages refs #23734

diff --git src/hg/makeDb/doc/asmHubs/mkAsmStats.pl src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
index c6154f9..eaafb3c 100755
--- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
+++ src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
@@ -10,61 +10,63 @@
   printf STDERR "e.g.: mkAsmStats Mammals mammals\n";
   exit 255;
 }
 my $Name = shift;
 my $asmHubName = shift;
 
 my $home = $ENV{'HOME'};
 my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 
 my $commonNameList = "$asmHubName.asmId.commonName.tsv";
 my $commonNameOrder = "$asmHubName.commonName.asmId.orderList.tsv";
 my @orderList;	# asmId of the assemblies in order from the *.list files
 # the order to read the different .list files:
 my %betterName;	# key is asmId, value is better common name than found in
 		# assembly_report
+my $vgpIndex = 0;
+$vgpIndex = 1 if ($Name =~ m/vgp/i);
 
 my $assemblyTotal = 0;	# complete list of assemblies in this group
 my $asmCount = 0;	# count of assemblies completed and in the table
 my $overallNucleotides = 0;
 my $overallSeqCount = 0;
 my $overallGapSize = 0;
 my $overallGapCount = 0;
 
 ##############################################################################
 # 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
 }
 
 ##############################################################################
 ### start the HTML output
 ##############################################################################
 sub startHtml() {
 
 my $timeStamp = `date "+%F"`;
 chomp $timeStamp;
 
 my $subSetMessage = "subset of $asmHubName only";
 if ($asmHubName eq "vertebrate") {
    $subSetMessage = "subset of other ${asmHubName}s only";
 }
 
-if ($Name =~ m/vgp/i) {
+if ($vgpIndex) {
   print <<"END"
 <!DOCTYPE HTML 4.01 Transitional>
 <!--#set var="TITLE" value="VGP - Vertebrate Genomes Project assembly hubs, assembly statistics" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>VGP - Vertebrate Genomes Project assembly hubs, assembly statistics</h1>
 <p>
 <a href='https://vertebrategenomesproject.org/' target=_blank>
 <img src='VGPlogo.png' width=280 alt='VGP logo'></a></p>
 <p>
 This assembly hub contains assemblies released
 by the <a href='https://vertebrategenomesproject.org/' target=_blank>
 Vertebrate Genomes Project.</a>
@@ -144,31 +146,33 @@
 END
 } else {
   print <<"END"
 
 </tbody>
 </table>
 END
 }
 }	#	sub endTable()
 
 ##############################################################################
 ### end the HTML output
 ##############################################################################
 sub endHtml() {
 
-if ($asmHubName ne "viral") {
+# do not print these links for VGP index
+
+if ((0 == $vgpIndex) && ($asmHubName ne "viral")) {
   printf "<p>\n<table border='1'><thead>\n";
   printf "<tr><th colspan=6 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n";
   printf "<tr><th>Assembly hubs index pages:&nbsp;</th>\n";
   printf "<th><a href='../primates/index.html'>Primates</a></th>\n";
   printf "<th><a href='../mammals/index.html'>Mammals</a></th>\n";
   printf "<th><a href='../birds/index.html'>Birds</a></th>\n";
   printf "<th><a href='../fish/index.html'>Fish</a></th>\n";
   printf "<th><a href='../vertebrate/index.html'>other vertebrates</a></th>\n";
 
   printf "</tr><tr>\n";
   printf "<th>Hubs assembly statistics:&nbsp;</th>\n";
   printf "<th><a href='../primates/asmStats.html'>Primates</a></th>\n";
   printf "<th><a href='../mammals/asmStats.html'>Mammals</a></th>\n";
   printf "<th><a href='../birds/asmStats.html'>Birds</a></th>\n";
   printf "<th><a href='../fish/asmStats.html'>Fish</a></th>\n";
@@ -322,31 +326,31 @@
     }
     close (FH);
     my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$accessionDir/$accessionId";
     printf "<tr><td align=right>%d</td>\n", ++$asmCount;
 #    printf "<td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=%s/hub.txt&amp;genome=%s&amp;position=lastDbPos' target=_blank>%s</a></td>\n", $hubUrl, $accessionId, $commonName;
     printf "<td align=center><a href='https://genome.ucsc.edu/h/%s' target=_blank>%s</a></td>\n", $accessionId, $commonName;
     printf "    <td align=center><a href='%s/' target=_blank>%s</a></td>\n", $hubUrl, $sciName;
     printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s/' target=_blank>%s</a></td>\n", $accessionId, $asmId;
     printf "    <td align=right>%s</td>\n", commify($seqCount);
     printf "    <td align=right>%s</td>\n", commify($totalSize);
     printf "    <td align=right>%s</td>\n", commify($gapCount);
     printf "    <td align=right>%s</td>\n", commify($gapSize);
     printf "    <td align=right>%.2f</td>\n", $maskPerCent;
     printf "</tr>\n";
   }
-}
+}	#	sub tableContents()
 
 ##############################################################################
 ### main()
 ##############################################################################
 
 open (FH, "<$toolsDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp $line;
   my ($commonName, $asmId) = split('\t', $line);
   push @orderList, $asmId;
   $betterName{$asmId} = $commonName;
   ++$assemblyTotal;
 }
 close (FH);