980db7f979bf44931256f421017262d2983f6aa1
hiram
  Sat Sep 24 18:39:43 2022 -0700
correct blank line after output and get queryDate and queryAsmName up a level so they can be used in all sections refs #29982

diff --git src/hg/utils/automation/asmHubChainNetTrackDb.pl src/hg/utils/automation/asmHubChainNetTrackDb.pl
index 6a19109..e6e8402 100755
--- src/hg/utils/automation/asmHubChainNetTrackDb.pl
+++ src/hg/utils/automation/asmHubChainNetTrackDb.pl
@@ -23,31 +23,31 @@
 
 my $buildDir = shift;
 my $targetDb = basename($buildDir);
 my @queryList;
 
 open (DL, "ls -d $buildDir/trackData/lastz.*|") or die "can not list $buildDir/trackData/lastz.*";
 while (my $lastzDir = <DL>) {
   chomp $lastzDir;
   my $queryDb = basename($lastzDir);
   $queryDb =~ s/lastz.//;
   push @queryList, $queryDb;
 }
 close (DL);
 
 # foreach my $queryDb (@queryList) {
-#  printf "%s vs. %s\n", $queryDb, $targetDb;
+#    printf STDERR "%s vs. %s\n", $queryDb, $targetDb;
 # }
 
 ##### begin trackDb output ######
 printf "track %sChainNet\n", $targetDb;
 printf "compositeTrack on
 shortLabel Chain/Net
 longLabel Chain and Net alignments to target sequence: %s\n", $targetDb;
 printf "subGroup1 view Views chain=Chains net=Nets\n";
 printf "subGroup2 species Species";
 my $N = 0;
 foreach my $queryDb (@queryList) {
   printf " s%03d=%s", $N++, $queryDb;
 }
 printf "\n";
 printf "subGroup3 clade Clade c00=human\n";
@@ -180,110 +180,113 @@
 
 printf "
     track %sMafNetViewnet
     shortLabel Nets
     view net
     visibility dense
     subTrack %sChainNet
 ", $targetDb, $targetDb;
 
 $N = 0;
 $chainNetPriority = 1;
 foreach my $queryDb (@queryList) {
   my @targetAccession = split('_', $targetDb);
   my $targetAcc = sprintf("%s_%s", $targetAccession[0], $targetAccession[1]);
   my $QueryDb = ucfirst($queryDb);
+  my $queryDate = "some date";
+  my $queryAsmName = "";
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.net.bb`;
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.net.summary.bb`;
-  if ( -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.bb) {
-printf STDERR "constructing net.bb links\n";
+  if ( -s "../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.bb" ) {
+printf STDERR "constructing net.bb links $targetDb $queryDb\n";
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.bb  $buildDir/bbi/$targetDb.${queryDb}.net.bb`;
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.net.summary.bb`;
-  my $queryDate = "some date";
-  my $queryAsmName = "";
   if ( $queryDb !~ m/^GC/ ) {
     $queryDate = `hgsql -N -e 'select description from dbDb where name="$queryDb"' hgcentraltest | sed -e 's/ (.*//;'`;
     chomp $queryDate;
   } else {
     ($queryDate, $queryAsmName) = &HgAutomate::hubDateName($queryDb);
   }
     printf "
         track net%s
         parent %sMafNetViewnet
         subGroups view=net species=s%03d clade=c00
         shortLabel %s mafNet
         longLabel %s%s (%s) mafNet Alignment
         type bigMaf
         bigDataUrl bbi/%s.%s.net.bb
         summary bbi/%s.%s.net.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %d
 ", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;
   }
 
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.synNet.bb`;
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.synNet.summary.bb`;
   if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.bb" ) {
-printf STDERR "constructing synNet.bb links\n";
+printf STDERR "constructing synNet.bb links $targetDb $queryDb\n";
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.bb  $buildDir/bbi/$targetDb.${queryDb}.synNet.bb`;
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.synNet.summary.bb`;
     printf "
         track synNet%s
         parent %sMafNetViewnet
         subGroups view=net species=s%03d clade=c00
         shortLabel %s synNet
         longLabel %s%s (%s) Syntenic Net Alignment
         type bigMaf
         bigDataUrl bbi/%s.%s.synNet.bb
         summary bbi/%s.%s.synNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %d
 ", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;
 
   }
 
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.rbestNet.bb`;
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.rbestNet.summary.bb`;
   if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.bb" ) {
-printf STDERR "constructing rbestNet.bb links\n";
+printf STDERR "constructing rbestNet.bb links $targetDb $queryDb\n";
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.bb  $buildDir/bbi/$targetDb.${queryDb}.rbestNet.bb`;
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.rbestNet.summary.bb`;
     printf "
         track rbestNet%s
         parent %sMafNetViewnet
         subGroups view=net species=s%03d clade=c00
         shortLabel %s rbestNet
         longLabel %s%s (%s) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl bbi/%s.%s.rbestNet.bb
         summary bbi/%s.%s.rbestNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %d
 ", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;
 
   }
 
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.bb`;
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.summary.bb`;
   if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.bb" ) {
+printf STDERR "constructing liftOverNet links $targetDb $queryDb\n";
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.bb  $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.bb`;
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.summary.bb`;
     printf "
         track liftOverNet%s
         parent %sMafNetViewnet
         subGroups view=net species=s%03d clade=c00
         shortLabel %s liftOverNet
         longLabel %s%s (%s) Lift Over Net Alignment
         type bigMaf
         bigDataUrl bbi/%s.%s.liftOverNet.bb
         summary bbi/%s.%s.liftOverNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %d
 ", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;
 
   }
   $N++;
 }
+
+printf "\n" if ($N > 0);