#!/usr/bin/perl

@sexes = ("M", "F");
@ages = ("E14", "E16");
@reps = ("1", "2", "3");

$ltPink = "255,102,178";  # female E14.5
$dkPink = "255,0,127";    # female E16.5
$ltBlue = "0,128,255";    # male E14.5
$dkBlue = "0,0,204";	  # male E16.5
%useColor = ("E14M" => $ltBlue, "E16M" => $dkBlue, "E14F" => $ltPink, "E16F" => $dkPink);

open(OUT, ">trackDb.RNA.txt");
$prio = 500;

##### normalized depth #####
# write header supertrack header
print OUT "track\tdataRNAseq\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tRNAseq\n";
print OUT "longLabel\tRNA-seq data (normalized depth)\n";
print OUT "priority\t$prio\n";
print OUT "subGroup1\tview View NORM=normDepth\n";
print OUT "subGroup2\tSex Sex M=M F=F\n";
print OUT "subGroup3\tAge Age E14=E14.5 E16=E16.5\n";
print OUT "subGroup4\tRep Rep 1=1 2=2 3=3\n";
print OUT "dimensions\tdimX=Sex dimY=Age dimA=Rep\n";
print OUT "sortOrder\tSex=+ Age=+ Rep=+\n";
print OUT "type\tbigWig\n\n";

# write header for depth tracks
print OUT "   track\tdataRNAseq_ViewDepth\n";
print OUT "   parent\tdataRNAseq\n";
print OUT "   shortLabel\tRNAseq\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\t150:30:11\n";
print OUT "   viewLimits\t0:100\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# write depth tracks
foreach $mf (@sexes) { foreach $age (@ages) { foreach $r (@reps) {
  $id = "$age$mf\-$r";
  $bwfile = "data/RNAseq/$id.depthNorm.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  $xx = "$age$mf";
  $thiscolor = $useColor{$xx};
  print OUT "      track\t$id.RNA\n";
  print OUT "      parent\tdataRNAseq_ViewDepth\n";
  print OUT "      bigDataUrl\t$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$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tSex=$mf Age=$age Rep=$r view=NORM\n\n";
} } }
print OUT "\n\n";


close(OUT);