#!/usr/bin/perl

@grps = ("Gli1", "Amhr2");
@reps = ("1", "2", "3");
@strands = ("plus", "minus");

%useColor = ("Gli1" => "153,0,70", "Amhr2" => "204,102,0");

open(OUT, ">trackDb.RNA-Amhr2.txt");
$prio = 700;

##### normalized depth #####
# write header supertrack header
print OUT "track\tdataRNAseqAm\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tRNAseq Amhr2\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\tCell Cell G=Gli1 A=Amhr2\n";
print OUT "subGroup3\tStrand Strand plus=plus minus=minus\n";
print OUT "subGroup4\tRep Rep 1=1 2=2 3=3\n";
print OUT "dimensions\tdimX=Cell dimY=Rep dimA=Strand\n";
print OUT "sortOrder\tCell=+ Rep=+ Strand=+\n";
print OUT "type\tbigWig\n\n";

# write header for depth tracks
print OUT "   track\tdataRNAseqAm_ViewDepth\n";
print OUT "   parent\tdataRNAseqAm\n";
print OUT "   shortLabel\tRNAseq Amhr2\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 $grp (@grps) { foreach $r (@reps) { foreach $str (@strands) {
  $id = "$grp\-$r";
  $s = uc(substr($str, 0, 1));
  $c = uc(substr($grp, 0, 1));
  $bwfile = "data/RNAseq_Amhr2/$id.depthNorm.$str.bw";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  print OUT "      track\t$id.RNA.$s\n";
  print OUT "      parent\tdataRNAseqAm_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id RNAseq, $str\n";
  print OUT "      longLabel\tnormalized RNA-seq depth: $id ($str)\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$useColor{$grp}\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tCell=$c Rep=$r Strand=$str view=NORM\n\n";
} } }
print OUT "\n\n";


close(OUT);