#!/usr/bin/perl

@grps = ("mES","CN","WT");
@reps = ("1", "2");

#$thiscolor = "0,0,204";
$thiscolor = "0,0,0";

open(OUT, ">trackDb.RNA-Nell2_oe.txt");
$prio = 100;

##### normalized depth #####
# write header supertrack header
print OUT "track\tdataRNAseqNell2oe\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tRNAseqCNoe\n";
print OUT "longLabel\tNell2-overexpr 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 $gt (@grps) { print OUT " $gt=$gt"; } print OUT "\n";
print OUT "subGroup3\tRep Rep"; foreach $r (@reps) { print OUT " $r=$r"; } 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\tdataRNAseqNell2oe_ViewDepth\n";
print OUT "   parent\tdataRNAseqNell2oe\n";
print OUT "   shortLabel\tRNAseqCNoe\n";
print OUT "   longLabel\tRNA-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\t150:40:11\n";
print OUT "   viewLimits\t0:500\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# write depth tracks
foreach $gt (@grps) { foreach $r (@reps) {
  $id = "$gt\-$r";
  $bwfile = "data/$id.depthNorm.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  print OUT "      track\t$id.RNA\n";
  print OUT "      parent\tdataRNAseqNell2oe_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id RNAseq\n";
  print OUT "      longLabel\tnormalized RNA-seq depth: $id\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$thiscolor\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tGroup=$gt Rep=$r view=NORM\n\n";
} }
print OUT "\n\n";


close(OUT);