src/hg/makeDb/doc/asmHubs/mkAsmStats.pl cdd0101336b3399e8d1a204a298b017a2675cc3a

cdd0101336b3399e8d1a204a298b017a2675cc3a
hiram
  Fri Jan 24 10:35:41 2020 -0800
now correctly using this asmHubs directories as toolsDir to obtain commonName listings refs #24748

diff --git src/hg/makeDb/doc/asmHubs/mkAsmStats.pl src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
index 223ac45..06f6e58 100755
--- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
+++ src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
@@ -2,73 +2,76 @@
 
 use strict;
 use warnings;
 use File::stat;
 
 my $argc = scalar(@ARGV);
 if ($argc != 2) {
   printf STDERR "mkAsmStats Name asmName\n";
   printf STDERR "e.g.: mkAsmStats Mammals mammals\n";
   exit 255;
 }
 my $Name = shift;
 my $asmHubName = shift;
 
 my $home = $ENV{'HOME'};
-my $srcDocDir = "${asmHubName}AsmHub";
-my $asmHubDocDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir";
+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 $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 ${asmHubName}s only";
+}
+
 print <<"END"
 <!DOCTYPE HTML 4.01 Transitional>
 <!--#set var="TITLE" value="$Name genomes assembly hubs" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>$Name Genomes assembly hubs</h1>
 <p>
-Assemblies from NCBI/Genbank/Refseq sources, subset of $asmHubName only.
+Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
 </p>
 
 <h3>See also: <a href='index.html'>hub access</a></h3><br>
 
 <h3>Data resource links</h3>
 NOTE: <em>Click on the column headers to sort the table by that column</em><br>
 The <em>link to genome browser</em> will attach only that single assembly to
 the genome browser.
 END
 }
 
 ##############################################################################
 ### start the table output
 ##############################################################################
 sub startTable() {
@@ -264,29 +267,29 @@
     printf "    <td align=center><a href='https://hgdownload.soe.ucsc.edu/hubs/%s/genomes/%s/' target=_blank>%s</a></td>\n", $asmHubName, $asmId, $sciName;
     printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s</a></td>\n", $gcPrefix, $asmAcc, $asmId;
     printf "    <td align=right>%s</td>\n", commify($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";
   }
 }
 
 ##############################################################################
 ### main()
 ##############################################################################
 
-open (FH, "<$asmHubDocDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
+open (FH, "<$toolsDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
 while (my $line = <FH>) {
   chomp $line;
   my ($commonName, $asmId) = split('\t', $line);
   push @orderList, $asmId;
   ++$assemblyTotal;
 }
 close (FH);
 
 startHtml();
 startTable();
 tableContents();
 endTable();
 endHtml();