#!/usr/bin/perl

# Kilsoo Jeon's data, reanalyzed Nov2021

$datadir = "data/KJeon-astro-NS50708-RNAseq";
$trackname = "trackDb.KJeon-astro-NS50708-Nov2021-RNAseq.txt";
$stroot = "RNA02";
$shortLab = "KJeon-ASI-NS50708";

@grps = ("ASI_24hr_GLIS3","ASI_24hr_GLIS3KO","ASI_24hr_H9");
@reps = (1,2);
#@strands = ("plus","minus");

$prio = 150;
$useColor = "0,0,0";



open(OUT, ">$trackname");

##### normalized depth #####
# write header supertrack header
print OUT "track\tdata$stroot\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\t$shortLab RNAseq\n";
print OUT "longLabel\t$shortLab RNA-seq data (normalized depth)\n";
print OUT "priority\t$prio\n";
print OUT "subGroup1\tview View NORM=normDepth\n";
print OUT "subGroup2\tGroup Group"; foreach $grp (@grps) { print OUT " $grp=$grp"; } print OUT "\n";
print OUT "subGroup3\tRep Rep"; foreach $r (@reps) { print OUT " $r=$r"; } print OUT "\n";
#print OUT "subGroup4\tStrand Strand"; foreach $str (@strands) { print OUT " $str=$str"; } print OUT "\n";
print OUT "dimensions\tdimX=Group dimY=Rep\n";
print OUT "sortOrder\tGroup=+ Rep=+\n";
print OUT "type\tbigWig\n\n";

# write header for depth tracks
print OUT "   track\tdata$stroot\_ViewDepth\n";
print OUT "   parent\tdata$stroot\n";
print OUT "   shortLabel\t$shortLab RNAseq\n";
print OUT "   longLabel\t$shortLab RNA-seq data (normalized depth)\n";
print OUT "   view\tNORM\n";
print OUT "   visibility\tfull\n";
print OUT "   type\tbigWig\n";
print OUT "   allButtonPair\ton\n";
print OUT "   centerLabelsDense\ton\n";
print OUT "   dragAndDrop\ton\n";
print OUT "   alwaysZero\ton\n";
print OUT "   graphTypeDefault\tbar\n";
print OUT "   maxHeightPixels\t150:30:11\n";
print OUT "   viewLimits\t0:5\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# write depth tracks
foreach $grp (@grps) { foreach $r (@reps) { # foreach $str (@strands) {
  $id = "$grp\-$r";
  $bwfile = "$datadir/$id.depthRPM.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; next; }
  $prio++;
  print OUT "      track\t$id.$stroot\n";
  print OUT "      parent\tdata$stroot\_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id RNAseq\n";
  print OUT "      longLabel\tnormalized RNA-seq depth: $id\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$useColor\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tGroup=$grp Rep=$r view=NORM\n\n";
} } # }
print OUT "\n\n";


close(OUT);