#!/usr/bin/perl

@gts = ("BecKO", "BecWT");
@reps = ("1", "2", "3");

$myColorATAC = "0,0,153";

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

##### supertrack1: normalized depth  #####
# write header supertrack header
$prio = 200;
print OUT "track\tdataNorm\n";
print OUT "compositeTrack\ton\n";
print OUT "shortLabel\tATACseqNorm\n";
print OUT "longLabel\tATAC-seq data (normalized depth)\n";
print OUT "priority\t$prio\n";
print OUT "subGroup1\tView View NRM=normDepth\n";
print OUT "subGroup2\tGenotype Genotype"; foreach $gt (@gts) { 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=Rep dimY=Gentype\n";
print OUT "sortOrder\tGenotype=+ Rep=+\n";
print OUT "type\tbigWig\n\n";

# write header for normalized depth tracks
print OUT "   track\tdataNorm_ViewDepth\n";
print OUT "   parent\tdataNorm\n";
print OUT "   shortLabel\tFootprints\n";
print OUT "   longLabel\tATAC-seq footprints (normalized)\n";
print OUT "   view\tNRM\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 normalized depth tracks
foreach $gt (@gts) { foreach $r (@reps) {
  $id = "$gt$r";
  $bwfile = "DATA/$id.mm10.footprint.norm100M.bigWig";
  unless (-e $bwfile) { print "WARNING: Did not find $bwfile.\n"; exit; }
  $prio++;
  print OUT "      track\t$id.DN\n";
  print OUT "      parent\tdataNorm_ViewDepth\n";
  print OUT "      bigDataUrl\t$bwfile\n";
  print OUT "      shortLabel\t$id\n";
  print OUT "      longLabel\tfootprints depth: $id\n";
  print OUT "      type\tbigWig\n";
  print OUT "      color\t$myColorATAC\n";
  print OUT "      priority\t$prio\n";
  print OUT "      visibility\thide\n";
  print OUT "      subGroups\tGenotype=$gt Rep=$r View=NRM\n\n";
} }


##### supertrack2: unified peaks (color-coded); currently on 1 track here  #####
# write header supertrack header
$prio = 200;
print OUT "track\tdataPeaksU\n";
print OUT "superTrack\ton show\n";
print OUT "shortLabel\tpeaks\n";
print OUT "longLabel\tpeak tracks\n\n";

$bbfile = "DATA/KOvsWT.minOV3.minLen50.byColor.bigBed";
unless (-e $bbfile) { print "WARNING: Did not find $bbfile; exiting.\n"; exit; }
  print OUT "    track\tpeaks\n";
  print OUT "    parent\tdataPeaksU\n";
  print OUT "    type\tbigBed 9\n";
  print OUT "    bigDataUrl\t$bbfile\n";
  print OUT "    shortLabel\tpeaks\n";
  print OUT "    longLabel\tunified peaks, color-coded by differential status\n";
  print OUT "    priority\t$prio\n";
  print OUT "    visibility\tdense\n";
  print OUT "    itemRgb\ton\n\n";



close(OUT);