ed7414028de9887b9fe8d562758a0af09dedcd8f
hiram
  Thu May 23 18:31:52 2024 -0700
better default visibilities no redmine

diff --git src/hg/utils/automation/asmHubChainNetTrackDb.pl src/hg/utils/automation/asmHubChainNetTrackDb.pl
index 792cfb1..57a013e 100755
--- src/hg/utils/automation/asmHubChainNetTrackDb.pl
+++ src/hg/utils/automation/asmHubChainNetTrackDb.pl
@@ -1,354 +1,361 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use File::Basename;
 use FindBin qw($Bin);
 use lib "$Bin";
 use HgAutomate;
 
 sub usage() {
   printf STDERR "usage: asmHubChainNetTrackDb.pl <buildDir>\n";
   printf STDERR "expecting to find directories: buildDir/trackData/lastz.*/\n";
   printf STDERR "where each /lastz.*/ directory is one completed lastz/chainNet\n";
   printf STDERR "and basename(buildDir) is the 'target' sequence name\n";
   exit 255;
 }
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 1) {
   usage;
 }
 
 my $buildDir = shift;
 my $targetDb = basename($buildDir);
 my @tParts = split('_', $targetDb);
 my $targetAccession = "$tParts[0]_$tParts[1]";
 my @queryList;
 my %queryPrio;	# key is queryDb, value is featureBits on chain file
 my %commonName;	# key is queryDb, value is common name
 
 open (my $CN, "-|", "hgsql -N -e 'select gcAccession,commonName from genark;' hgcentraltest") or die "can not hgsql -N -e 'select gcAccession,commonName from genark;'";
 while (my $line = <$CN>) {
   chomp $line;
   my ($gcX, $comName) = split('\t', $line);
   $comName =~ s/\s\(.*//;
   $commonName{$gcX} = $comName;
 }
 close ($CN);
 
 open ($CN, "-|", "hgsql -N -e 'select name,organism from dbDb;' hgcentraltest") or die "can not hgsql -N -e 'select name,organism from dbDb;'";
 while (my $line = <$CN>) {
   chomp $line;
   my ($gcX, $comName) = split('\t', $line);
   $comName =~ s/\s\(.*//;
   $commonName{$gcX} = "$comName/${gcX}";
 }
 close ($CN);
 
 `mkdir -p $buildDir/bbi`;
 `mkdir -p $buildDir/liftOver`;
 
 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.//;
   my $Qdb = ucfirst($queryDb);
 #  push @queryList, $queryDb;
   $queryPrio{$queryDb} = 100;
   my $fbTxt = `ls $buildDir/trackData/lastz.${queryDb}/fb.${targetAccession}.chain${Qdb}Link.txt 2> /dev/null`;
   chomp $fbTxt;
   if (-s "${fbTxt}") {
     my $prio = `cut -d' ' -f5 $fbTxt | tr -d '()%'`;
     chomp $prio;
 #    $queryPrio{$queryDb} = sprintf("%d", int((100 - $prio)+0.5));
     $queryPrio{$queryDb} = sprintf("%.3f", 100 - $prio);
   }
 }
 close (DL);
 
 foreach my $qDb ( sort {$queryPrio{$a} <=> $queryPrio{$b}} keys %queryPrio) {
   push @queryList, $qDb;
 }
 
 # foreach my $queryDb (@queryList) {
 #    printf STDERR "%s vs. %s\n", $queryDb, $targetDb;
 # }
 
 ##### begin trackDb output ######
 printf "track %sChainNet\n", $targetDb;
 printf "compositeTrack on
 shortLabel Chain/Net
 longLabel Chain alignments to target sequence: %s\n", $targetDb;
 printf "subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment\n";
 printf "subGroup2 species Assembly";
 my $N = 0;
 foreach my $queryDb (@queryList) {
   printf " s%03d=%s", $N++, $queryDb;
 }
 printf "\n";
 printf "subGroup3 chainType chain_type c00=chain c01=syntenic c02=reciprocal_best c03=lift_over c04=chain_align c05=syntenic_align c06=reciprocal_align c07=lift_over_align\n";
 printf "dragAndDrop subTracks\n";
 printf "visibility hide
 group compGeno
 color 0,0,0
 altColor 255,255,0
 type bed 3
 chainLinearGap loose
 chainMinScore 5000
 dimensions dimensionX=chainType dimensionY=species
 sortOrder species=+ view=+ chainType=+
 configurable on\n";
 printf "html html/%s.chainNet\n", $targetDb;
 
 printf "
     track %sChainNetViewchain
     shortLabel Chains
     view chain
-    visibility pack
-    subTrack %sChainNet
+    visibility dense
+    parent %sChainNet
     spectrum on
 
     track %sChainNetViewSynTen
     shortLabel Syntenic
     view synten
-    visibility pack
-    subTrack %sChainNet
+    visibility hide
+    parent %sChainNet
     spectrum on
 
     track %sChainNetViewRBest
     shortLabel Reciprocal best
     view rbest
-    visibility pack
-    subTrack %sChainNet
+    visibility hide
+    parent %sChainNet
     spectrum on
 
     track %sChainNetViewLiftOver
     shortLabel Lift over
     view liftover
-    visibility pack
-    subTrack %sChainNet
+    visibility hide
+    parent %sChainNet
     spectrum on
 ", $targetDb, $targetDb, $targetDb, $targetDb, $targetDb, $targetDb, $targetDb, $targetDb;
 
 $N = 0;
 foreach my $queryDb (@queryList) {
   my $comName = $queryDb;
   $comName = $commonName{$queryDb} if (defined($commonName{$queryDb}));
   my $QueryDb = ucfirst($queryDb);
   my $overChain="${targetAccession}.${queryDb}.over.chain.gz";
   my $overToChain="${targetAccession}To${QueryDb}.over.chain.gz";
   my $lastzDir="lastz.$queryDb";
   `rm -f $buildDir/bbi/$targetDb.chain${QueryDb}.bb`;
   `rm -f $buildDir/bbi/$targetDb.chain${QueryDb}Link.bb`;
   `rm -f $buildDir/liftOver/${overToChain}`;
   if ( -s "$buildDir/trackData/$lastzDir/axtChain/${overChain}" ) {
      `ln -s ../trackData/$lastzDir/axtChain/${overChain} $buildDir/liftOver/${overToChain}`;
   } else {
      printf STDERR "# NOT FOUND: '%s'\n", "$buildDir/trackData/$lastzDir/axtChain/${overChain}";
   }
   `ln -s ../trackData/lastz.$queryDb/axtChain/chain${QueryDb}.bb  $buildDir/bbi/$targetDb.chain${QueryDb}.bb`;
   `ln -s ../trackData/lastz.$queryDb/axtChain/chain${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chain${QueryDb}Link.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);
   }
+  if (0 == $N) {
+    printf "
+        track chain%s
+        parent %sChainNetViewchain on", $QueryDb, $targetDb;
+  } else {
     printf "
         track chain%s
-        subTrack %sChainNetViewchain off
+        parent %sChainNetViewchain off", $QueryDb, $targetDb;
+  }
+  printf "
         subGroups view=chain species=s%03d chainType=c00
         shortLabel %s Chain
         longLabel %s/%s%s (%s) Chained Alignments
         type bigChain %s
         bigDataUrl bbi/%s.chain%s.bb
         linkDataUrl bbi/%s.chain%sLink.bb
         otherDb %s
         html html/%s.chainNet
         priority %s
-", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
+", $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
      $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $queryPrio{$queryDb};
 
   if ( -s "$buildDir/trackData/lastz.$queryDb/axtChain/chainSyn${QueryDb}.bb" ) {
     `rm -f $buildDir/bbi/$targetDb.chainSyn${QueryDb}.bb`;
     `rm -f $buildDir/bbi/$targetDb.chainSyn${QueryDb}Link.bb`;
     `ln -s ../trackData/lastz.$queryDb/axtChain/chainSyn${QueryDb}.bb  $buildDir/bbi/$targetDb.chainSyn${QueryDb}.bb`;
     `ln -s ../trackData/lastz.$queryDb/axtChain/chainSyn${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chainSyn${QueryDb}Link.bb`;
   printf "
         track chainSyn%s
-        subTrack %sChainNetViewSynTen off
+        parent %sChainNetViewSynTen off
         subGroups view=synten species=s%03d chainType=c01
         shortLabel %s synChain
         longLabel %s/%s%s (%s) Chained Alignments
         type bigChain %s
         bigDataUrl bbi/%s.chainSyn%s.bb
         linkDataUrl bbi/%s.chainSyn%sLink.bb
         otherDb %s
         html html/%s.chainNet
         priority %s
 ", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
      $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $queryPrio{$queryDb};
 
   }
 
   if ( -s "$buildDir/trackData/lastz.$queryDb/axtChain/chainRBest${QueryDb}.bb" ) {
     `rm -f $buildDir/bbi/$targetDb.chainRBest${QueryDb}.bb`;
     `rm -f $buildDir/bbi/$targetDb.chainRBest${QueryDb}Link.bb`;
     `ln -s ../trackData/lastz.$queryDb/axtChain/chainRBest${QueryDb}.bb  $buildDir/bbi/$targetDb.chainRBest${QueryDb}.bb`;
     `ln -s ../trackData/lastz.$queryDb/axtChain/chainRBest${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chainRBest${QueryDb}Link.bb`;
   printf "
         track chainRBest%s
-        subTrack %sChainNetViewRBest off
+        parent %sChainNetViewRBest off
         subGroups view=rbest species=s%03d chainType=c02
         shortLabel %s rbChain
         longLabel %s/%s%s (%s) Chained Alignments
         type bigChain %s
         bigDataUrl bbi/%s.chainRBest%s.bb
         linkDataUrl bbi/%s.chainRBest%sLink.bb
         otherDb %s
         html html/%s.chainNet
         priority %s
 ", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
      $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $queryPrio{$queryDb};
 
   }
 
   if ( -s "$buildDir/trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}.bb" ) {
     `rm -f $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}.bb`;
     `rm -f $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}Link.bb`;
     `ln -s ../trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}.bb  $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}.bb`;
     `ln -s ../trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}Link.bb`;
 
   printf "
         track chainLiftOver%s
-        subTrack %sChainNetViewLiftOver off
+        parent %sChainNetViewLiftOver off
         subGroups view=liftover species=s%03d chainType=c03
         shortLabel %s loChain
         longLabel %s/%s%s (%s) Chained Alignments
         type bigChain %s
         bigDataUrl bbi/%s.chainLiftOver%s.bb
         linkDataUrl bbi/%s.chainLiftOver%sLink.bb
         otherDb %s
         html html/%s.chainNet
         priority %s
 ", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
      $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $queryPrio{$queryDb};
 
   }
   $N++;
 }
 
 printf "
     track %sMafNetViewnet
     shortLabel Nets
     view align
-    visibility dense
-    subTrack %sChainNet
+    visibility hide
+    parent %sChainNet
 ", $targetDb, $targetDb;
 
 $N = 0;
 foreach my $queryDb (@queryList) {
   my $comName = $queryDb;
   $comName = $commonName{$queryDb} if (defined($commonName{$queryDb}));
   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.${queryDb}.net.summary.bb`;
   if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.bb" ) {
   `ln -s ../trackData/lastz.$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`;
   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
+        parent %sMafNetViewnet off
         subGroups view=align species=s%03d chainType=c04
         shortLabel %s mafNet
         longLabel %s/%s%s (%s) Chained Alignments
         type bigMaf
         bigDataUrl bbi/%s.%s.net.bb
         summary bbi/%s.%s.net.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %s
 ", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $queryPrio{$queryDb};
   }
   `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}.${queryDb}.synNet.bb" ) {
   `ln -s ../trackData/lastz.$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
+        parent %sMafNetViewnet off
         subGroups view=align species=s%03d chainType=c05
         shortLabel %s synNet
         longLabel %s/%s%s (%s) Chained Alignments
         type bigMaf
         bigDataUrl bbi/%s.%s.synNet.bb
         summary bbi/%s.%s.synNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %s
 ", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $queryPrio{$queryDb};
 
   }
 
   `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}.${queryDb}.rbestNet.bb" ) {
   `ln -s ../trackData/lastz.$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
+        parent %sMafNetViewnet off
         subGroups view=align species=s%03d chainType=c06
         shortLabel %s rbestNet
         longLabel %s/%s%s (%s) Chained Alignments
         type bigMaf
         bigDataUrl bbi/%s.%s.rbestNet.bb
         summary bbi/%s.%s.rbestNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %s
 ", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $queryPrio{$queryDb};
 
   }
 
   `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
+        parent %sMafNetViewnet off
         subGroups view=align species=s%03d chainType=c07
         shortLabel %s liftOverNet
         longLabel %s/%s%s (%s) Chained Alignments
         type bigMaf
         bigDataUrl bbi/%s.%s.liftOverNet.bb
         summary bbi/%s.%s.liftOverNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %s
 ", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $queryPrio{$queryDb}
 
   }
   $N++;
 }
 
 printf "\n" if ($N > 0);