#!/usr/bin/perl

# E-MTAB-4616

@ages = ("11.5", "12.5", "14.5", "15.5", "16.5", "18.5");
@sexes = ("Female-XX", "Male-XY");
@cells = ("Germ", "Somatic");

$dkPink = "255,0,127";    # female
$dkBlue = "0,0,204";	  # male
%useColor = ("Male-XY" => $dkBlue, "Female-XX" => $dkPink);

open(OUT, ">trackDb.RNA-public.txt");
$prio = 200;

##### normalized depth #####
# write header supertrack header
print OUT "track\tdataRNAseqPublic\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tRNAseq E-MTAB-4616\n";
print OUT "longLabel\tRNA-seq data E-MTAB-4616 (aggregate normalized depth)\n";
print OUT "priority\t$prio\n";
print OUT "subGroup1\tview View NORM=normDepth\n";
print OUT "subGroup2\tCell Cell"; foreach $ct (@cells) { print OUT " $ct=$ct"; } print OUT "\n";
print OUT "subGroup3\tAge Age"; foreach $a (@ages) { print OUT " E$a=E$a"; } print OUT "\n";
print OUT "subGroup4\tSex Sex"; foreach $s (@sexes) { print OUT " $s=$s"; } print OUT "\n";
print OUT "dimensions\tdimX=Sex dimY=Age dimA=Cell\n";
print OUT "sortOrder\tCell=+ Sex=+ Age=+\n";
print OUT "type\tbigWig\n\n";

# write header for depth tracks
print OUT "   track\tdataRNAseqPublic_ViewDepth\n";
print OUT "   parent\tdataRNAseqPublic\n";
print OUT "   shortLabel\tRNAseq E-MTAB-4616\n";
print OUT "   longLabel\tRNA-seq data E-MTAB-4616 (aggregate 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\t0:500\n";
print OUT "   showSubtrackColorOnUi\ton\n";
print OUT "   viewUi\ton\n\n";

# write depth tracks
foreach $ct (@cells) { foreach $age (@ages) { foreach $mf (@sexes) {
  $id = "$ct\-Day$age\-$mf";
  $bwfile = "DATA/$id.depthNorm.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  $thiscolor = $useColor{$mf};
  print OUT "      track\t$id.RNA\n";
  print OUT "      parent\tdataRNAseqPublic_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id\n";
  print OUT "      longLabel\taggregate normalized RNA-seq depth: $id\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$thiscolor\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tCell=$ct Age=E$age Sex=$mf view=NORM\n\n";
} } }
print OUT "\n\n";


close(OUT);