afee0fcf2a7b7de2eb37e1420dc126607373453e
hiram
  Wed May 27 17:31:45 2020 -0700
rework scripts to allow subset hubs to be created from a list of assemblies refs #23734

diff --git src/hg/makeDb/doc/asmHubs/mkAsmStats.pl src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
index 85afdfa..881e100 100755
--- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
+++ src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
@@ -1,39 +1,40 @@
 #!/usr/bin/env perl
 
 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";
+if ($argc != 3) {
+  printf STDERR "mkAsmStats Name asmHubName [two column name list]\n";
+  printf STDERR "e.g.: mkAsmStats Mammals mammals mammals.asmId.commonName.tsv\n";
+  printf STDERR "the name list is found in \$HOME/kent/src/hg/makeDb/doc/asmHubs/\n";
+  printf STDERR "\nthe two columns are 1: asmId (accessionId_assemblyName)\n";
+  printf STDERR "column 2: common name for species, columns separated by tab\n";
   exit 255;
 }
 my $Name = shift;
 my $asmHubName = shift;
+my $commonNameOrder = 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 @orderList;	# asmId of the assemblies in order from the commonNameOrder file
+my %commonName;	# key is asmId, value is a common name, perhaps more appropriate
+                # than found in assembly_report file
 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 $_[0];
@@ -240,31 +241,32 @@
   my ($buildDir, $asmId) = @_;
   my $gapBed = "$buildDir/trackData/allGaps/$asmId.allGaps.bed.gz";
   my $gapCount = 0;
   if ( -s "$gapBed" ) {
     $gapCount = `zcat $gapBed | awk '{print \$3-\$2}' | ave stdin | grep '^count' | awk '{print \$2}'`;
   }
   chomp $gapCount;
   return ($gapCount);
 }
 
 ##############################################################################
 ### tableContents()
 ##############################################################################
 sub tableContents() {
 
-  foreach my $asmId (reverse(@orderList)) {
+  foreach my $asmId (@orderList) {
+printf STDERR "# asmId: '%s'\n", $asmId;
     my ($gcPrefix, $asmAcc, $asmName) = split('_', $asmId, 3);
     my $accessionId = sprintf("%s_%s", $gcPrefix, $asmAcc);
     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";
     }
     my $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
     if (! -s "$asmReport") {
       printf STDERR "# no assembly report:\n# %s\n", $asmReport;
       next;
     }
@@ -315,31 +317,31 @@
            $bioSample =~ s/.*:\s+//;
         }
       } elsif ($line =~ m/BioProject:/) {
         if ($bioProject =~ m/notFound/) {
            ++$itemsFound;
            $bioProject = $line;
            $bioProject =~ s/.*:\s+//;
         }
       } elsif ($line =~ m/Organism name:/) {
         if ($sciName =~ m/notFound/) {
            ++$itemsFound;
            $commonName = $line;
            $sciName = $line;
            $commonName =~ s/.*\(//;
            $commonName =~ s/\)//;
-           $commonName = $betterName{$asmId} if (exists($betterName{$asmId}));
+           $commonName = $commonName{$asmId} if (exists($commonName{$asmId}));
            $sciName =~ s/.*:\s+//;
            $sciName =~ s/\s+\(.*//;
         }
       } elsif ($line =~ m/Taxid:/) {
         if ($taxId =~ m/notFound/) {
            ++$itemsFound;
            $taxId = $line;
            $taxId =~ s/.*:\s+//;
         }
       }
     }
     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, $commonName;
@@ -351,27 +353,27 @@
     printf "    <td align=right>%s</td>\n", commify($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', $line);
+  my ($asmId, $commonName) = split('\t', $line);
   push @orderList, $asmId;
-  $betterName{$asmId} = $commonName;
+  $commonName{$asmId} = $commonName;
   ++$assemblyTotal;
 }
 close (FH);
 
 startHtml();
 startTable();
 tableContents();
 endTable();
 endHtml();