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/trackData.pl src/hg/makeDb/doc/asmHubs/trackData.pl
index 71fe9ff..ab7922d 100755
--- src/hg/makeDb/doc/asmHubs/trackData.pl
+++ src/hg/makeDb/doc/asmHubs/trackData.pl
@@ -1,53 +1,55 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use File::stat;
 
 my $argc = scalar(@ARGV);
-if ($argc < 2) {
-  printf STDERR "usage: trackData.pl Name asmHubName > trackData.html\n";
-  printf STDERR "e.g.: trackData.pl Mammals mammals > trackData.html\n";
+if ($argc < 3) {
+  printf STDERR "usage: trackData.pl Name asmHubName [two column name list] > trackData.html\n";
+  printf STDERR "e.g.: trackData.pl Mammals mammals mammals.asmId.commonName.tsv > trackData.html\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 $testOutput = 0;
 my $spliceOut = -1;
 
 if ($argc > 2) {
   for (my $i = 0; $i < $argc; ++$i) {
     if ($ARGV[$i] =~ /-test/) {
       $testOutput = 1;
       $spliceOut = $i;
     }
   }
 }
 if ($spliceOut != -1) {
   splice @ARGV, $spliceOut, 1;
 }
 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
+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
 		# 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($) {
@@ -340,31 +342,31 @@
   my $asmCounted = 0;
   if ($testOutput) {  # add extra columns during 'test' output
 #                       0          1          2        3       4      5    6
 #  7       8      9            10           11        12          13
 #     14
 # my @trackList = qw(ncbiRefSeq xenoRefGene augustus ensGene gc5Base gap allGaps assembly rmsk simpleRepeat windowMasker gapOverlap tandemDups cpgIslandExtUnmasked cpgIslandExt);
 #                       0            1         2        3       4      5      6
 #      7      8           9               10
 # my @trackList = qw(ncbiRefSeq xenoRefGene augustus ensGene gc5Base allGaps assembly rmsk simpleRepeat windowMasker cpgIslandExtUnmasked);
     splice @trackList, 11, 0, "cpgIslandExt";
     splice @trackList, 10, 0, "tandemDups";
     splice @trackList, 10, 0, "gapOverlap";
     splice @trackList, 5, 0, "gap";
     splice @trackList, 1, 0, "ncbiGene";
   }
-  foreach my $asmId (reverse(@orderList)) {
+  foreach my $asmId (@orderList) {
     my $tracksCounted = 0;
     my ($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 $trackDb="$buildDir/${asmId}.trackDb.txt";
     next if (! -s "$trackDb");	# assembly build not complete
     my $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
     if (! -s "$asmReport") {
@@ -405,31 +407,31 @@
       $line =~ s/
//g;;
       $line =~ s/\s+$//g;;
       if ($line =~ m/Date:/) {
         if ($asmDate =~ m/notFound/) {
            ++$itemsFound;
            $asmDate = $line;
            $asmDate =~ s/.*:\s+//;
         }
       } elsif ($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+\(.*//;
         }
       }
     }
     close (FH);
     my $hubUrl = "https://genome.ucsc.edu/h/$accessionId";
     if ($testOutput) {
       $hubUrl = "https://genome-test.gi.ucsc.edu/h/$accessionId";
     }
     printf "<tr><td align=right>%d</td>\n", ++$asmCount;
     printf "<td align=center><a href='%s' target=_blank>%s<br>%s</a></td>\n", $hubUrl, $commonName, $accessionId;
     foreach my $track (@trackList) {
       my $trackFile = "$buildDir/bbi/$asmId.$track";
       my $trackFb = "$buildDir/trackData/$track/fb.$asmId.$track.txt";
@@ -493,27 +495,27 @@
     }	#	foreach my $track (@trackList)
     printf "</tr>\n";
     $asmCounted += 1;
     printf STDERR "# %03d\t%02d tracks\t%s\n", $asmCounted, $tracksCounted, $asmId;
   }
 }
 
 ##############################################################################
 ### 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();